6YX8

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.

PDB DOI: https://doi.org/10.2210/pdb6YX8/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Nostoc sp. WR13
Mutation(s): No

Deposited: 2020-04-30 Released: 2021-05-12
Deposition Author(s): Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.
Funding Organization(s): Department of Energy (DOE, United States), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.198
R-Value Work: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13

Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 116.82 kDa
Atom Count: 9,412
Modelled Residue Count: 963
Deposited Residue Count: 963
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN	A [auth AAA], C [auth CCC], E [auth EEE]	160	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW22 (Nostoc sp. WR13) Explore A0A4Y5PW22 Go to UniProtKB: A0A4Y5PW22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4Y5PW22
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN	B [auth BBB], D [auth DDD], F [auth FFF]	161	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW23 (Nostoc sp. WR13) Explore A0A4Y5PW23 Go to UniProtKB: A0A4Y5PW23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4Y5PW23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PXQ (Subject of Investigation/LOI) Query on PXQ Download Ideal Coordinates CCD File SDF format, chain JC [auth FFF] SDF format, chain G [auth AAA] SDF format, chain OA [auth CCC] SDF format, chain RB [auth EEE] SDF format, chain W [auth BBB] SDF format, chain ZA [auth DDD] MOL2 format, chain JC [auth FFF] MOL2 format, chain G [auth AAA] MOL2 format, chain OA [auth CCC] MOL2 format, chain RB [auth EEE] MOL2 format, chain W [auth BBB] MOL2 format, chain ZA [auth DDD]	G [auth AAA] JC [auth FFF] OA [auth CCC] RB [auth EEE] W [auth BBB] G [auth AAA], JC [auth FFF], OA [auth CCC], RB [auth EEE], W [auth BBB], ZA [auth DDD]	3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C₃₃ H₄₂ N₄ O₆ RIXXCMVADHNPLY-UKJJQICTSA-N		Interactions Focus chain G [auth AAA] Focus chain JC [auth FFF] Focus chain OA [auth CCC] Focus chain RB [auth EEE] Focus chain W [auth BBB] Focus chain ZA [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain JC [auth FFF] Focus chain OA [auth CCC] Focus chain RB [auth EEE] Focus chain W [auth BBB] Focus chain ZA [auth DDD]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain J [auth AAA] SDF format, chain BA [auth BBB] SDF format, chain MA [auth BBB] SDF format, chain OC [auth FFF] MOL2 format, chain AA [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain BA [auth BBB] MOL2 format, chain MA [auth BBB] MOL2 format, chain OC [auth FFF]	AA [auth BBB], BA [auth BBB], J [auth AAA], MA [auth BBB], OC [auth FFF]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain J [auth AAA] Focus chain MA [auth BBB] Focus chain OC [auth FFF] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain J [auth AAA] Focus chain MA [auth BBB] Focus chain OC [auth FFF]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain EB [auth DDD] SDF format, chain FB [auth DDD] SDF format, chain GB [auth DDD] SDF format, chain QB [auth EEE] SDF format, chain TB [auth EEE] MOL2 format, chain EB [auth DDD] MOL2 format, chain FB [auth DDD] MOL2 format, chain GB [auth DDD] MOL2 format, chain QB [auth EEE] MOL2 format, chain TB [auth EEE]	EB [auth DDD], FB [auth DDD], GB [auth DDD], QB [auth EEE], TB [auth EEE]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EB [auth DDD] Focus chain FB [auth DDD] Focus chain GB [auth DDD] Focus chain QB [auth EEE] Focus chain TB [auth EEE] Interactions & Density Focus chain EB [auth DDD] Focus chain FB [auth DDD] Focus chain GB [auth DDD] Focus chain QB [auth EEE] Focus chain TB [auth EEE]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain DB [auth DDD] SDF format, chain I [auth AAA] MOL2 format, chain DB [auth DDD] MOL2 format, chain I [auth AAA]	DB [auth DDD], I [auth AAA]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain DB [auth DDD] Focus chain I [auth AAA] Interactions & Density Focus chain DB [auth DDD] Focus chain I [auth AAA]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain DA [auth BBB] SDF format, chain IC [auth EEE] SDF format, chain U [auth AAA] SDF format, chain CA [auth BBB] SDF format, chain K [auth AAA] SDF format, chain PC [auth FFF] SDF format, chain QA [auth CCC] SDF format, chain QC [auth FFF] SDF format, chain RC [auth FFF] SDF format, chain SC [auth FFF] SDF format, chain UB [auth EEE] MOL2 format, chain DA [auth BBB] MOL2 format, chain IC [auth EEE] MOL2 format, chain U [auth AAA] MOL2 format, chain CA [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain PC [auth FFF] MOL2 format, chain QA [auth CCC] MOL2 format, chain QC [auth FFF] MOL2 format, chain RC [auth FFF] MOL2 format, chain SC [auth FFF] MOL2 format, chain UB [auth EEE]	CA [auth BBB] DA [auth BBB] IC [auth EEE] K [auth AAA] PC [auth FFF] CA [auth BBB], DA [auth BBB], IC [auth EEE], K [auth AAA], PC [auth FFF], QA [auth CCC], QC [auth FFF], RC [auth FFF], SC [auth FFF], U [auth AAA], UB [auth EEE]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain IC [auth EEE] Focus chain K [auth AAA] Focus chain PC [auth FFF] Focus chain QA [auth CCC] Focus chain QC [auth FFF] Focus chain RC [auth FFF] Focus chain SC [auth FFF] Focus chain U [auth AAA] Focus chain UB [auth EEE] Interactions & Density Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain IC [auth EEE] Focus chain K [auth AAA] Focus chain PC [auth FFF] Focus chain QA [auth CCC] Focus chain QC [auth FFF] Focus chain RC [auth FFF] Focus chain SC [auth FFF] Focus chain U [auth AAA] Focus chain UB [auth EEE]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain SB [auth EEE] MOL2 format, chain SB [auth EEE]	SB [auth EEE]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain SB [auth EEE] Interactions & Density Focus chain SB [auth EEE]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain AB [auth DDD] SDF format, chain BB [auth DDD] SDF format, chain LC [auth FFF] SDF format, chain X [auth BBB] SDF format, chain Y [auth BBB] SDF format, chain CB [auth DDD] SDF format, chain H [auth AAA] SDF format, chain KC [auth FFF] SDF format, chain MC [auth FFF] SDF format, chain NC [auth FFF] SDF format, chain PA [auth CCC] SDF format, chain Z [auth BBB] MOL2 format, chain AB [auth DDD] MOL2 format, chain BB [auth DDD] MOL2 format, chain LC [auth FFF] MOL2 format, chain X [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain CB [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain KC [auth FFF] MOL2 format, chain MC [auth FFF] MOL2 format, chain NC [auth FFF] MOL2 format, chain PA [auth CCC] MOL2 format, chain Z [auth BBB]	AB [auth DDD] BB [auth DDD] CB [auth DDD] H [auth AAA] KC [auth FFF] AB [auth DDD], BB [auth DDD], CB [auth DDD], H [auth AAA], KC [auth FFF], LC [auth FFF], MC [auth FFF], NC [auth FFF], PA [auth CCC], X [auth BBB], Y [auth BBB], Z [auth BBB]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AB [auth DDD] Focus chain BB [auth DDD] Focus chain CB [auth DDD] Focus chain H [auth AAA] Focus chain KC [auth FFF] Focus chain LC [auth FFF] Focus chain MC [auth FFF] Focus chain NC [auth FFF] Focus chain PA [auth CCC] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB] Interactions & Density Focus chain AB [auth DDD] Focus chain BB [auth DDD] Focus chain CB [auth DDD] Focus chain H [auth AAA] Focus chain KC [auth FFF] Focus chain LC [auth FFF] Focus chain MC [auth FFF] Focus chain NC [auth FFF] Focus chain PA [auth CCC] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth AAA] SDF format, chain RA [auth CCC] SDF format, chain SA [auth CCC] SDF format, chain TC [auth FFF] SDF format, chain YB [auth EEE] SDF format, chain EA [auth BBB] SDF format, chain FA [auth BBB] SDF format, chain GA [auth BBB] SDF format, chain HB [auth DDD] SDF format, chain IB [auth DDD] SDF format, chain JB [auth DDD] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain O [auth AAA] SDF format, chain TA [auth CCC] SDF format, chain UA [auth CCC] SDF format, chain UC [auth FFF] SDF format, chain VB [auth EEE] SDF format, chain VC [auth FFF] SDF format, chain WB [auth EEE] SDF format, chain WC [auth FFF] SDF format, chain XA [auth CCC] SDF format, chain XB [auth EEE] MOL2 format, chain N [auth AAA] MOL2 format, chain RA [auth CCC] MOL2 format, chain SA [auth CCC] MOL2 format, chain TC [auth FFF] MOL2 format, chain YB [auth EEE] MOL2 format, chain EA [auth BBB] MOL2 format, chain FA [auth BBB] MOL2 format, chain GA [auth BBB] MOL2 format, chain HB [auth DDD] MOL2 format, chain IB [auth DDD] MOL2 format, chain JB [auth DDD] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain TA [auth CCC] MOL2 format, chain UA [auth CCC] MOL2 format, chain UC [auth FFF] MOL2 format, chain VB [auth EEE] MOL2 format, chain VC [auth FFF] MOL2 format, chain WB [auth EEE] MOL2 format, chain WC [auth FFF] MOL2 format, chain XA [auth CCC] MOL2 format, chain XB [auth EEE]	EA [auth BBB] FA [auth BBB] GA [auth BBB] HB [auth DDD] IB [auth DDD] EA [auth BBB], FA [auth BBB], GA [auth BBB], HB [auth DDD], IB [auth DDD], JB [auth DDD], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], RA [auth CCC], SA [auth CCC], TA [auth CCC], TC [auth FFF], UA [auth CCC], UC [auth FFF], VB [auth EEE], VC [auth FFF], WB [auth EEE], WC [auth FFF], XA [auth CCC], XB [auth EEE], YB [auth EEE]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth BBB] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain HB [auth DDD] Focus chain IB [auth DDD] Focus chain JB [auth DDD] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain RA [auth CCC] Focus chain SA [auth CCC] Focus chain TA [auth CCC] Focus chain TC [auth FFF] Focus chain UA [auth CCC] Focus chain UC [auth FFF] Focus chain VB [auth EEE] Focus chain VC [auth FFF] Focus chain WB [auth EEE] Focus chain WC [auth FFF] Focus chain XA [auth CCC] Focus chain XB [auth EEE] Focus chain YB [auth EEE] Interactions & Density Focus chain EA [auth BBB] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain HB [auth DDD] Focus chain IB [auth DDD] Focus chain JB [auth DDD] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain RA [auth CCC] Focus chain SA [auth CCC] Focus chain TA [auth CCC] Focus chain TC [auth FFF] Focus chain UA [auth CCC] Focus chain UC [auth FFF] Focus chain VB [auth EEE] Focus chain VC [auth FFF] Focus chain WB [auth EEE] Focus chain WC [auth FFF] Focus chain XA [auth CCC] Focus chain XB [auth EEE] Focus chain YB [auth EEE]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AC [auth EEE] SDF format, chain AD [auth FFF] SDF format, chain BC [auth EEE] SDF format, chain DC [auth EEE] SDF format, chain EC [auth EEE] SDF format, chain FC [auth EEE] SDF format, chain HC [auth EEE] SDF format, chain KB [auth DDD] SDF format, chain P [auth AAA] SDF format, chain PB [auth DDD] SDF format, chain Q [auth AAA] SDF format, chain T [auth AAA] SDF format, chain XC [auth FFF] SDF format, chain YC [auth FFF] SDF format, chain ZB [auth EEE] SDF format, chain ZC [auth FFF] SDF format, chain CC [auth EEE] SDF format, chain GC [auth EEE] SDF format, chain HA [auth BBB] SDF format, chain IA [auth BBB] SDF format, chain JA [auth BBB] SDF format, chain KA [auth BBB] SDF format, chain LA [auth BBB] SDF format, chain LB [auth DDD] SDF format, chain MB [auth DDD] SDF format, chain NA [auth CCC] SDF format, chain NB [auth DDD] SDF format, chain OB [auth DDD] SDF format, chain R [auth AAA] SDF format, chain S [auth AAA] SDF format, chain V [auth AAA] SDF format, chain VA [auth CCC] SDF format, chain WA [auth CCC] SDF format, chain YA [auth DDD] MOL2 format, chain AC [auth EEE] MOL2 format, chain AD [auth FFF] MOL2 format, chain BC [auth EEE] MOL2 format, chain DC [auth EEE] MOL2 format, chain EC [auth EEE] MOL2 format, chain FC [auth EEE] MOL2 format, chain HC [auth EEE] MOL2 format, chain KB [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain PB [auth DDD] MOL2 format, chain Q [auth AAA] MOL2 format, chain T [auth AAA] MOL2 format, chain XC [auth FFF] MOL2 format, chain YC [auth FFF] MOL2 format, chain ZB [auth EEE] MOL2 format, chain ZC [auth FFF] MOL2 format, chain CC [auth EEE] MOL2 format, chain GC [auth EEE] MOL2 format, chain HA [auth BBB] MOL2 format, chain IA [auth BBB] MOL2 format, chain JA [auth BBB] MOL2 format, chain KA [auth BBB] MOL2 format, chain LA [auth BBB] MOL2 format, chain LB [auth DDD] MOL2 format, chain MB [auth DDD] MOL2 format, chain NA [auth CCC] MOL2 format, chain NB [auth DDD] MOL2 format, chain OB [auth DDD] MOL2 format, chain R [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain V [auth AAA] MOL2 format, chain VA [auth CCC] MOL2 format, chain WA [auth CCC] MOL2 format, chain YA [auth DDD]	AC [auth EEE] AD [auth FFF] BC [auth EEE] CC [auth EEE] DC [auth EEE] AC [auth EEE], AD [auth FFF], BC [auth EEE], CC [auth EEE], DC [auth EEE], EC [auth EEE], FC [auth EEE], GC [auth EEE], HA [auth BBB], HC [auth EEE], IA [auth BBB], JA [auth BBB], KA [auth BBB], KB [auth DDD], LA [auth BBB], LB [auth DDD], MB [auth DDD], NA [auth CCC], NB [auth DDD], OB [auth DDD], P [auth AAA], PB [auth DDD], Q [auth AAA], R [auth AAA], S [auth AAA], T [auth AAA], V [auth AAA], VA [auth CCC], WA [auth CCC], XC [auth FFF], YA [auth DDD], YC [auth FFF], ZB [auth EEE], ZC [auth FFF]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth EEE] Focus chain AD [auth FFF] Focus chain BC [auth EEE] Focus chain CC [auth EEE] Focus chain DC [auth EEE] Focus chain EC [auth EEE] Focus chain FC [auth EEE] Focus chain GC [auth EEE] Focus chain HA [auth BBB] Focus chain HC [auth EEE] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain KB [auth DDD] Focus chain LA [auth BBB] Focus chain LB [auth DDD] Focus chain MB [auth DDD] Focus chain NA [auth CCC] Focus chain NB [auth DDD] Focus chain OB [auth DDD] Focus chain P [auth AAA] Focus chain PB [auth DDD] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain V [auth AAA] Focus chain VA [auth CCC] Focus chain WA [auth CCC] Focus chain XC [auth FFF] Focus chain YA [auth DDD] Focus chain YC [auth FFF] Focus chain ZB [auth EEE] Focus chain ZC [auth FFF] Interactions & Density Focus chain AC [auth EEE] Focus chain AD [auth FFF] Focus chain BC [auth EEE] Focus chain CC [auth EEE] Focus chain DC [auth EEE] Focus chain EC [auth EEE] Focus chain FC [auth EEE] Focus chain GC [auth EEE] Focus chain HA [auth BBB] Focus chain HC [auth EEE] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain KB [auth DDD] Focus chain LA [auth BBB] Focus chain LB [auth DDD] Focus chain MB [auth DDD] Focus chain NA [auth CCC] Focus chain NB [auth DDD] Focus chain OB [auth DDD] Focus chain P [auth AAA] Focus chain PB [auth DDD] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain V [auth AAA] Focus chain VA [auth CCC] Focus chain WA [auth CCC] Focus chain XC [auth FFF] Focus chain YA [auth DDD] Focus chain YC [auth FFF] Focus chain ZB [auth EEE] Focus chain ZC [auth FFF]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	B [auth BBB], D [auth DDD], F [auth FFF]	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.198
R-Value Work: 0.160
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.676	α = 90
b = 177.34	β = 90
c = 122.416	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)	India	BT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)	India	BT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description