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- PDB-8vtn: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -

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Basic information

Entry
Database: PDB / ID: 8vtn
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-nitrophenylalanine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / membrane protein / electron transfer
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily ...Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / SPHEROIDENE / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsTran, K. / Mathews, I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Department of Energy (DOE, United States) United States
CitationJournal: J.Phys.Chem.B / Year: 2025
Title: Application of Amber Suppression To Study the Role of Tyr M210 in Electron Transfer in Rhodobacter sphaeroides Photosynthetic Reaction Centers.
Authors: Tran, K.N. / Faries, K.M. / Magdaong, N.C.M. / Mathews, I.I. / Weaver, J.B. / Kirsh, J.M. / Holten, D. / Kirmaier, C. / Boxer, S.G.
History
DepositionJan 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,34916
Polymers91,1123
Non-polymers8,23713
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.490, 141.490, 187.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Reaction center protein ... , 3 types, 3 molecules HLM

#1: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 26022.904 Da / Num. of mol.: 1 / Fragment: UNP residues 11-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: puhA / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufL / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 33742.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufM / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 8 types, 15 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O
#10: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.63 Å3/Da / Density % sol: 78.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.4-1.5 M potassium phosphate reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 250 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 3.57→37.45 Å / Num. obs: 26248 / % possible obs: 99.55 % / Redundancy: 7.8 % / Biso Wilson estimate: 87.25 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.3124 / Rpim(I) all: 0.1147 / Rrim(I) all: 0.328 / Net I/σ(I): 6.66
Reflection shellResolution: 3.57→3.698 Å / Redundancy: 8 % / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2593 / CC1/2: 0.659 / CC star: 0.86 / Rpim(I) all: 0.5076 / Rrim(I) all: 1.543 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.57→37.45 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1317 5.02 %
Rwork0.211 --
obs0.2127 26239 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.57→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6740 0 249 2 6991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047257
X-RAY DIFFRACTIONf_angle_d0.7419947
X-RAY DIFFRACTIONf_dihedral_angle_d13.1961099
X-RAY DIFFRACTIONf_chiral_restr0.0421011
X-RAY DIFFRACTIONf_plane_restr0.0061238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.57-3.710.34681430.28362753X-RAY DIFFRACTION100
3.71-3.880.31440.24822696X-RAY DIFFRACTION99
3.88-4.090.26911440.23582742X-RAY DIFFRACTION99
4.09-4.340.24981440.2072728X-RAY DIFFRACTION100
4.34-4.680.22511490.18932754X-RAY DIFFRACTION100
4.68-5.150.231480.19062773X-RAY DIFFRACTION100
5.15-5.890.22541440.20342790X-RAY DIFFRACTION100
5.89-7.410.25571500.20822786X-RAY DIFFRACTION100
7.41-37.450.22021510.19892900X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 82.3222 Å / Origin y: -18.9352 Å / Origin z: 34.3716 Å
111213212223313233
T0.7395 Å20.0693 Å20.0229 Å2-0.5169 Å2-0.0187 Å2--0.4941 Å2
L1.6005 °2-0.2131 °2-0.5861 °2-0.7283 °20.0822 °2--0.9823 °2
S-0.0172 Å °-0.0106 Å °0.0225 Å °0.002 Å °0.0443 Å °-0.0165 Å °-0.0725 Å °0.0014 Å °-0.0189 Å °
Refinement TLS groupSelection details: all

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