7Q7P | pdb_00007q7p

LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE

PDB DOI: https://doi.org/10.2210/pdb7Q7P/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2021-11-09 Released: 2022-06-22
Deposition Author(s): Baath, P., Banacore, A., Neutze, R.
Funding Organization(s): National Research Development and Innovation Office (NKFIH), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.165 (Depositor), 0.175 (DCC)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre.

Bath, P., Banacore, A., Borjesson, P., Bosman, R., Wickstrand, C., Safari, C., Dods, R., Ghosh, S., Dahl, P., Ortolani, G., Bjorg Ulfarsdottir, T., Hammarin, G., Garcia Bonete, M.J., Vallejos, A., Ostojic, L., Edlund, P., Linse, J.B., Andersson, R., Nango, E., Owada, S., Tanaka, R., Tono, K., Joti, Y., Nureki, O., Luo, F., James, D., Nass, K., Johnson, P.J.M., Knopp, G., Ozerov, D., Cirelli, C., Milne, C., Iwata, S., Branden, G., Neutze, R.

(2022) Acta Crystallogr D Struct Biol 78: 698-708

PubMed: 35647917 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798322004144
Primary Citation Related Structures:
7Q7P, 7Q7Q

PubMed Abstract:
Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile Q _B pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.

Organizational Affiliation

Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden.

Macromolecule Content

Total Structure Weight: 147.36 kDa
Atom Count: 10,442
Modeled Residue Count: 1,175
Deposited Residue Count: 1,210
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth CCC]	356	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07173
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	B [auth HHH]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	C [auth LLL]	273	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	D [auth MMM]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download:Ideal Coordinates CCD File SDF format, chain AA [auth MMM] SDF format, chain BA [auth MMM] SDF format, chain N [auth LLL] SDF format, chain M [auth LLL] MOL2 format, chain AA [auth MMM] MOL2 format, chain BA [auth MMM] MOL2 format, chain N [auth LLL] MOL2 format, chain M [auth LLL] mmCIF format, chain AA [auth MMM] mmCIF format, chain BA [auth MMM] mmCIF format, chain N [auth LLL] mmCIF format, chain M [auth LLL]	AA [auth MMM], BA [auth MMM], M [auth LLL], N [auth LLL]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain AA [auth MMM] Focus chain BA [auth MMM] Focus chain M [auth LLL] Focus chain N [auth LLL] Interactions & Density Focus chain AA [auth MMM] Focus chain BA [auth MMM] Focus chain M [auth LLL] Focus chain N [auth LLL]
BPB Query on BPB Download:Ideal Coordinates CCD File SDF format, chain CA [auth MMM] SDF format, chain O [auth LLL] MOL2 format, chain CA [auth MMM] MOL2 format, chain O [auth LLL] mmCIF format, chain CA [auth MMM] mmCIF format, chain O [auth LLL]	CA [auth MMM], O [auth LLL]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain CA [auth MMM] Focus chain O [auth LLL] Interactions & Density Focus chain CA [auth MMM] Focus chain O [auth LLL]
MQ7 Query on MQ7 Download:Ideal Coordinates CCD File SDF format, chain Z [auth MMM] MOL2 format, chain Z [auth MMM] mmCIF format, chain Z [auth MMM]	Z [auth MMM]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain Z [auth MMM] Interactions & Density Focus chain Z [auth MMM]
DGA Query on DGA Download:Ideal Coordinates CCD File SDF format, chain I [auth CCC] MOL2 format, chain I [auth CCC] mmCIF format, chain I [auth CCC]	I [auth CCC]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain I [auth CCC] Interactions & Density Focus chain I [auth CCC]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain E [auth CCC] SDF format, chain F [auth CCC] SDF format, chain G [auth CCC] SDF format, chain H [auth CCC] MOL2 format, chain E [auth CCC] MOL2 format, chain F [auth CCC] MOL2 format, chain G [auth CCC] MOL2 format, chain H [auth CCC] mmCIF format, chain E [auth CCC] mmCIF format, chain F [auth CCC] mmCIF format, chain G [auth CCC] mmCIF format, chain H [auth CCC]	E [auth CCC], F [auth CCC], G [auth CCC], H [auth CCC]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth CCC] Focus chain F [auth CCC] Focus chain G [auth CCC] Focus chain H [auth CCC] Interactions & Density Focus chain E [auth CCC] Focus chain F [auth CCC] Focus chain G [auth CCC] Focus chain H [auth CCC]
NS5 Query on NS5 Download:Ideal Coordinates CCD File SDF format, chain DA [auth MMM] MOL2 format, chain DA [auth MMM] mmCIF format, chain DA [auth MMM]	DA [auth MMM]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain DA [auth MMM] Interactions & Density Focus chain DA [auth MMM]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain K [auth HHH] MOL2 format, chain K [auth HHH] mmCIF format, chain K [auth HHH]	K [auth HHH]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain K [auth HHH] Interactions & Density Focus chain K [auth HHH]
UQ1 Query on UQ1 Download:Ideal Coordinates CCD File SDF format, chain V [auth LLL] SDF format, chain U [auth LLL] MOL2 format, chain V [auth LLL] MOL2 format, chain U [auth LLL] mmCIF format, chain V [auth LLL] mmCIF format, chain U [auth LLL]	U [auth LLL], V [auth LLL]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain U [auth LLL] Focus chain V [auth LLL] Interactions & Density Focus chain U [auth LLL] Focus chain V [auth LLL]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain W [auth LLL] SDF format, chain HA [auth MMM] MOL2 format, chain W [auth LLL] MOL2 format, chain HA [auth MMM] mmCIF format, chain W [auth LLL] mmCIF format, chain HA [auth MMM]	HA [auth MMM], W [auth LLL]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain HA [auth MMM] Focus chain W [auth LLL] Interactions & Density Focus chain HA [auth MMM] Focus chain W [auth LLL]
HTO Query on HTO Download:Ideal Coordinates CCD File SDF format, chain EA [auth MMM] SDF format, chain FA [auth MMM] SDF format, chain J [auth HHH] SDF format, chain Q [auth LLL] SDF format, chain R [auth LLL] SDF format, chain S [auth LLL] SDF format, chain X [auth LLL] SDF format, chain P [auth LLL] SDF format, chain GA [auth MMM] MOL2 format, chain EA [auth MMM] MOL2 format, chain FA [auth MMM] MOL2 format, chain J [auth HHH] MOL2 format, chain Q [auth LLL] MOL2 format, chain R [auth LLL] MOL2 format, chain S [auth LLL] MOL2 format, chain X [auth LLL] MOL2 format, chain P [auth LLL] MOL2 format, chain GA [auth MMM] mmCIF format, chain EA [auth MMM] mmCIF format, chain FA [auth MMM] mmCIF format, chain J [auth HHH] mmCIF format, chain Q [auth LLL] mmCIF format, chain R [auth LLL] mmCIF format, chain S [auth LLL] mmCIF format, chain X [auth LLL] mmCIF format, chain P [auth LLL] mmCIF format, chain GA [auth MMM]	EA [auth MMM] FA [auth MMM] GA [auth MMM] J [auth HHH] P [auth LLL] EA [auth MMM], FA [auth MMM], GA [auth MMM], J [auth HHH], P [auth LLL], Q [auth LLL], R [auth LLL], S [auth LLL], X [auth LLL]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain EA [auth MMM] Focus chain FA [auth MMM] Focus chain GA [auth MMM] Focus chain J [auth HHH] Focus chain P [auth LLL] Focus chain Q [auth LLL] Focus chain R [auth LLL] Focus chain S [auth LLL] Focus chain X [auth LLL] Interactions & Density Focus chain EA [auth MMM] Focus chain FA [auth MMM] Focus chain GA [auth MMM] Focus chain J [auth HHH] Focus chain P [auth LLL] Focus chain Q [auth LLL] Focus chain R [auth LLL] Focus chain S [auth LLL] Focus chain X [auth LLL]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth MMM] SDF format, chain JA [auth MMM] SDF format, chain KA [auth MMM] SDF format, chain L [auth HHH] SDF format, chain LA [auth MMM] SDF format, chain T [auth LLL] MOL2 format, chain IA [auth MMM] MOL2 format, chain JA [auth MMM] MOL2 format, chain KA [auth MMM] MOL2 format, chain L [auth HHH] MOL2 format, chain LA [auth MMM] MOL2 format, chain T [auth LLL] mmCIF format, chain IA [auth MMM] mmCIF format, chain JA [auth MMM] mmCIF format, chain KA [auth MMM] mmCIF format, chain L [auth HHH] mmCIF format, chain LA [auth MMM] mmCIF format, chain T [auth LLL]	IA [auth MMM] JA [auth MMM] KA [auth MMM] L [auth HHH] LA [auth MMM] IA [auth MMM], JA [auth MMM], KA [auth MMM], L [auth HHH], LA [auth MMM], T [auth LLL]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth MMM] Focus chain JA [auth MMM] Focus chain KA [auth MMM] Focus chain L [auth HHH] Focus chain LA [auth MMM] Focus chain T [auth LLL] Interactions & Density Focus chain IA [auth MMM] Focus chain JA [auth MMM] Focus chain KA [auth MMM] Focus chain L [auth HHH] Focus chain LA [auth MMM] Focus chain T [auth LLL]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain Y [auth MMM] MOL2 format, chain Y [auth MMM] mmCIF format, chain Y [auth MMM]	Y [auth MMM]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain Y [auth MMM] Interactions & Density Focus chain Y [auth MMM]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	B [auth HHH]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.165 (Depositor), 0.175 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.9	α = 90
b = 125.3	β = 90
c = 182.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Baath, P.

Banacore, A.

Neutze, R.

Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	European Union	789030
European Research Council (ERC)	European Union	201500560

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release
Version 1.1: 2022-10-12
Changes: Derived calculations, Refinement description
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

7Q7P | pdb_00007q7p

LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE

Literature

Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)