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- PDB-8vtk: Crystal structure of R.sphaeroides Photosynthetic Reaction Center... -

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Basic information

Entry
Database: PDB / ID: 8vtk
TitleCrystal structure of R.sphaeroides Photosynthetic Reaction Center variant Y(M210)2-chlorophenylalanine
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 / UBIQUINONE-10 / 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: 3.07 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)99,97216
Polymers91,1013
Non-polymers8,87113
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32690 Å2
ΔGint-233 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.950, 140.950, 186.720
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: 33732.184 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 , 9 types, 32 molecules

#4: Chemical ChemComp-FE / FE (III) ION


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#10: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O
#11: 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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 78.14 %
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: 3.07→39.76 Å / Num. obs: 40589 / % possible obs: 99.87 % / Redundancy: 16.8 % / Biso Wilson estimate: 74.42 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2643 / Rpim(I) all: 0.06604 / Rrim(I) all: 0.269 / Net I/σ(I): 12.68
Reflection shellResolution: 3.07→3.18 Å / Redundancy: 17.7 % / Rmerge(I) obs: 2.075 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3968 / CC1/2: 0.621 / CC star: 0.867 / Rpim(I) all: 0.507 / Rrim(I) all: 2.238 / % possible all: 99.97

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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: 3.07→39.76 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 2034 5.01 %
Rwork0.1771 --
obs0.1789 40572 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 267 19 7008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127267
X-RAY DIFFRACTIONf_angle_d1.3859966
X-RAY DIFFRACTIONf_dihedral_angle_d14.3861094
X-RAY DIFFRACTIONf_chiral_restr0.0691012
X-RAY DIFFRACTIONf_plane_restr0.0111242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.140.3381340.27482518X-RAY DIFFRACTION100
3.14-3.220.26471330.25412533X-RAY DIFFRACTION100
3.22-3.310.26221310.23662529X-RAY DIFFRACTION100
3.31-3.40.30281330.21442534X-RAY DIFFRACTION100
3.4-3.510.28651350.20042553X-RAY DIFFRACTION100
3.51-3.640.22471360.19622543X-RAY DIFFRACTION100
3.64-3.780.211340.16882533X-RAY DIFFRACTION100
3.79-3.960.20551340.16042566X-RAY DIFFRACTION100
3.96-4.170.18461370.14612560X-RAY DIFFRACTION100
4.17-4.430.20261360.14532562X-RAY DIFFRACTION100
4.43-4.770.18141370.1412563X-RAY DIFFRACTION100
4.77-5.250.1941340.15662589X-RAY DIFFRACTION100
5.25-60.19961330.17572609X-RAY DIFFRACTION100
6-7.550.19261430.18232618X-RAY DIFFRACTION100
7.56-39.760.19831440.18242728X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -45.6975 Å / Origin y: 41.7444 Å / Origin z: 3.0511 Å
111213212223313233
T0.3786 Å2-0.1107 Å2-0.0101 Å2-0.3907 Å2-0.0175 Å2--0.3877 Å2
L0.8683 °2-0.1449 °2-0.2188 °2-1.3165 °20.4479 °2--1.1378 °2
S0.0458 Å °-0.0139 Å °0.0107 Å °0.0374 Å °-0.0057 Å °-0.0396 Å °-0.0659 Å °0.1011 Å °-0.046 Å °
Refinement TLS groupSelection details: all

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