6UG4 | pdb_00006ug4

Open Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

PDB DOI: https://doi.org/10.2210/pdb6UG4/pdb

Classification: METAL TRANSPORT
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-09-25 Released: 2020-08-05
Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Open Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Wu, R., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 75.24 kDa
Atom Count: 5,028
Modeled Residue Count: 563
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ryanodine receptor	A, B, C, D, E A, B, C, D, E, F	100	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 Gene Names: BT_2247
UniProt
Find proteins for Q8A5J2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5J2 Go to UniProtKB: Q8A5J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A5J2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFF (Subject of Investigation/LOI) Query on CFF Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain W [auth E] SDF format, chain Q [auth C] SDF format, chain H [auth A] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain W [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain W [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain H [auth A]	AA [auth F] BA [auth F] G [auth A] H [auth A] I [auth A] AA [auth F], BA [auth F], G [auth A], H [auth A], I [auth A], O [auth C], P [auth C], Q [auth C], W [auth E]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth D]	K [auth A], L [auth A], N [auth B], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	CA [auth F] DA [auth F] EA [auth F] J [auth A] M [auth B] CA [auth F], DA [auth F], EA [auth F], J [auth A], M [auth B], R [auth C], S [auth C], X [auth E], Y [auth E], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	U [auth D], V [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain U [auth D] Focus chain V [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.235 (Depositor), 0.236 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.201	α = 90
b = 84.201	β = 90
c = 229.704	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Wu, R.

Jedrzejczak, R.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references
Version 2.1: 2024-10-23
Changes: Structure summary