9VDX | pdb_00009vdx

Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform

PDB DOI: https://doi.org/10.2210/pdb9VDX/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Blastochloris viridis
Mutation(s): No

Deposited: 2025-06-09 Released: 2026-03-25
Deposition Author(s): Ghosh, S., Banacore, A., Neutze, R., Branden, G.
Funding Organization(s): European Research Council (ERC), Swedish Research Council, The Swedish Foundation for Strategic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.

Ghosh, S., Banacore, A., Norder, P., Bjelcic, M., Kabbinale, A., Nileshwar, P., Wehlander, G., de Sanctis, D., Basu, S., Orlans, J., Vallejos, A., Chavas, L.M.G., Neutze, R., Branden, G.

(2026) J Appl Crystallogr 59: 303-315

PubMed: 41959872 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1600576725011513
Primary Citation Related Structures:
9S39, 9TBL, 9UYR, 9VDJ, 9VDX

PubMed Abstract:
Fixed-target platforms provide convenient support for microcrystals during serial X-ray crystallography studies using synchrotron radiation. Here, we describe a simple user-friendly 3D-printed support where the crystals are sandwiched between two layers of thin X-ray-transparent membrane resulting in very low scattering background. The platform is compatible with magnetic mounting onto the standard goniometer of macromolecular crystallography beamlines. Our design utilizes a 96-well frame that facilitates hanging-drop experiments directly on the membrane using conventional crystallization plates, thereby eliminating multiple pipetting and crystal handling steps. Crystals can be enclosed in a sandwich and packed into 'cassettes', preventing the risk of the sample drying out during room-temperature transportation to synchrotron sources. The versatility of the platform is demonstrated by five structures solved using different crystallization and data-collection strategies. Lysozyme single-crystal rotational crystallography at room temperature is shown, as well as microcrystal serial data collection under cryogenic conditions. On-chip microcrystallization is illustrated by use of a photosynthetic reaction center as an example. Finally, serial crystallography data collection at room temperature from microcrystals of the membrane protein cytochrome c oxidase crystallized in lipidic cubic phase is presented.

Organizational Affiliation

Department of Chemistry and Molecular Biology Gothenburg University Sweden.

Macromolecule Content

Total Structure Weight: 145.67 kDa
Atom Count: 10,352
Modeled Residue Count: 1,186
Deposited Residue Count: 1,190
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 C]	336	Blastochloris viridis	Mutation(s): 0
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 H]	258	Blastochloris viridis	Mutation(s): 0
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 L]	273	Blastochloris viridis	Mutation(s): 0
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 M]	323	Blastochloris viridis	Mutation(s): 0
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 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB (Subject of Investigation/LOI) Query on BCB Download:Ideal Coordinates CCD File SDF format, chain DA [auth M] SDF format, chain EA [auth M] SDF format, chain T [auth L] SDF format, chain U [auth L] MOL2 format, chain DA [auth M] MOL2 format, chain EA [auth M] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] mmCIF format, chain DA [auth M] mmCIF format, chain EA [auth M] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L]	DA [auth M], EA [auth M], T [auth L], U [auth L]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain DA [auth M] Focus chain EA [auth M] Focus chain T [auth L] Focus chain U [auth L] Interactions & Density Focus chain DA [auth M] Focus chain EA [auth M] Focus chain T [auth L] Focus chain U [auth L]
BPB (Subject of Investigation/LOI) Query on BPB Download:Ideal Coordinates CCD File SDF format, chain FA [auth M] SDF format, chain V [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain V [auth L] mmCIF format, chain FA [auth M] mmCIF format, chain V [auth L]	FA [auth M], V [auth L]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain FA [auth M] Focus chain V [auth L] Interactions & Density Focus chain FA [auth M] Focus chain V [auth L]
MQ7 (Subject of Investigation/LOI) Query on MQ7 Download:Ideal Coordinates CCD File SDF format, chain CA [auth M] MOL2 format, chain CA [auth M] mmCIF format, chain CA [auth M]	CA [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain CA [auth M] Interactions & Density Focus chain CA [auth M]
DGA (Subject of Investigation/LOI) Query on DGA Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
NS5 (Subject of Investigation/LOI) Query on NS5 Download:Ideal Coordinates CCD File SDF format, chain GA [auth M] MOL2 format, chain GA [auth M] mmCIF format, chain GA [auth M]	GA [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain GA [auth M] Interactions & Density Focus chain GA [auth M]
LDA (Subject of Investigation/LOI) Query on LDA Download:Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain PA [auth M] SDF format, chain QA [auth M] SDF format, chain R [auth H] SDF format, chain W [auth L] SDF format, chain Y [auth L] SDF format, chain Z [auth M] MOL2 format, chain M [auth H] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth M] MOL2 format, chain R [auth H] MOL2 format, chain W [auth L] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth M] mmCIF format, chain M [auth H] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth M] mmCIF format, chain R [auth H] mmCIF format, chain W [auth L] mmCIF format, chain Y [auth L] mmCIF format, chain Z [auth M]	M [auth H] PA [auth M] QA [auth M] R [auth H] W [auth L] M [auth H], PA [auth M], QA [auth M], R [auth H], W [auth L], Y [auth L], Z [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain R [auth H] Focus chain W [auth L] Focus chain Y [auth L] Focus chain Z [auth M] Interactions & Density Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain R [auth H] Focus chain W [auth L] Focus chain Y [auth L] Focus chain Z [auth M]
HTO (Subject of Investigation/LOI) Query on HTO Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain X [auth L] SDF format, chain AA [auth M] MOL2 format, chain S [auth H] MOL2 format, chain X [auth L] MOL2 format, chain AA [auth M] mmCIF format, chain S [auth H] mmCIF format, chain X [auth L] mmCIF format, chain AA [auth M]	AA [auth M], S [auth H], X [auth L]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain AA [auth M] Focus chain S [auth H] Focus chain X [auth L] Interactions & Density Focus chain AA [auth M] Focus chain S [auth H] Focus chain X [auth L]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth M] SDF format, chain IA [auth M] SDF format, chain J [auth C] SDF format, chain JA [auth M] SDF format, chain K [auth C] SDF format, chain KA [auth M] SDF format, chain L [auth C] SDF format, chain LA [auth M] SDF format, chain MA [auth M] SDF format, chain N [auth H] SDF format, chain NA [auth M] SDF format, chain O [auth H] SDF format, chain OA [auth M] SDF format, chain P [auth H] SDF format, chain Q [auth H] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain J [auth C] MOL2 format, chain JA [auth M] MOL2 format, chain K [auth C] MOL2 format, chain KA [auth M] MOL2 format, chain L [auth C] MOL2 format, chain LA [auth M] MOL2 format, chain MA [auth M] MOL2 format, chain N [auth H] MOL2 format, chain NA [auth M] MOL2 format, chain O [auth H] MOL2 format, chain OA [auth M] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain HA [auth M] mmCIF format, chain IA [auth M] mmCIF format, chain J [auth C] mmCIF format, chain JA [auth M] mmCIF format, chain K [auth C] mmCIF format, chain KA [auth M] mmCIF format, chain L [auth C] mmCIF format, chain LA [auth M] mmCIF format, chain MA [auth M] mmCIF format, chain N [auth H] mmCIF format, chain NA [auth M] mmCIF format, chain O [auth H] mmCIF format, chain OA [auth M] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H]	HA [auth M] IA [auth M] J [auth C] JA [auth M] K [auth C] HA [auth M], IA [auth M], J [auth C], JA [auth M], K [auth C], KA [auth M], L [auth C], LA [auth M], MA [auth M], N [auth H], NA [auth M], O [auth H], OA [auth M], P [auth H], Q [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth M] Focus chain IA [auth M] Focus chain J [auth C] Focus chain JA [auth M] Focus chain K [auth C] Focus chain KA [auth M] Focus chain L [auth C] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain N [auth H] Focus chain NA [auth M] Focus chain O [auth H] Focus chain OA [auth M] Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain HA [auth M] Focus chain IA [auth M] Focus chain J [auth C] Focus chain JA [auth M] Focus chain K [auth C] Focus chain KA [auth M] Focus chain L [auth C] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain N [auth H] Focus chain NA [auth M] Focus chain O [auth H] Focus chain OA [auth M] Focus chain P [auth H] Focus chain Q [auth H]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain BA [auth M] MOL2 format, chain BA [auth M] mmCIF format, chain BA [auth M]	BA [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Interactions & Density Focus chain BA [auth M]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.8	α = 90
b = 223.8	β = 90
c = 113.5	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
CrystFEL	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	789030 and 963936
Swedish Research Council	Sweden	2017-06734, 2021-05662 and 2021-05981
Swedish Research Council	Sweden	2015-00560
The Swedish Foundation for Strategic Research	Sweden	ID17-0060

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release
Version 1.1: 2026-04-22
Changes: Database references
Version 2.0: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary

9VDX | pdb_00009vdx

Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform

Literature

A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.

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)