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

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Basic information

Entry
Database: PDB / ID: 8vtj
TitleCrystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-cyanophenylalanine
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: 2.81 Å
AuthorsMathews, I. / Tran, K. / 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)102,23617
Polymers93,1353
Non-polymers9,10014
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33530 Å2
ΔGint-236 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.290, 141.290, 187.180
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: 28066.322 Da / Num. of mol.: 1
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: 33722.746 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, 125 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-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-U10 / UBIQUINONE-10 / Coenzyme Q10


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: 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
#9: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 111 / 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: 5.48 Å3/Da / Density % sol: 77.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
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: 2.81→40 Å / Num. obs: 53054 / % possible obs: 99.8 % / Redundancy: 22.6 % / Biso Wilson estimate: 59.7 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2759 / Rpim(I) all: 0.05918 / Rrim(I) all: 0.281 / Net I/σ(I): 13.01
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 22.1 % / Rmerge(I) obs: 2.275 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 5188 / CC1/2: 0.69 / CC star: 0.876 / Rpim(I) all: 0.4899 / Rrim(I) all: 2.382 / % possible all: 99.3

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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: 2.81→39.85 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 2636 4.97 %
Rwork0.1705 --
obs0.1718 53035 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.57 Å2
Refinement stepCycle: LAST / Resolution: 2.81→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 201 111 7117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097267
X-RAY DIFFRACTIONf_angle_d1.0779962
X-RAY DIFFRACTIONf_dihedral_angle_d15.0631095
X-RAY DIFFRACTIONf_chiral_restr0.0571009
X-RAY DIFFRACTIONf_plane_restr0.0091237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.860.30571340.272588X-RAY DIFFRACTION99
2.86-2.920.2721400.24552609X-RAY DIFFRACTION100
2.92-2.980.29651350.23982628X-RAY DIFFRACTION100
2.98-3.040.26361400.2392626X-RAY DIFFRACTION100
3.04-3.110.2551400.22122642X-RAY DIFFRACTION100
3.11-3.190.23411360.20642608X-RAY DIFFRACTION100
3.19-3.270.19481380.1932647X-RAY DIFFRACTION100
3.27-3.370.19971390.16992637X-RAY DIFFRACTION100
3.37-3.480.21511370.15522635X-RAY DIFFRACTION100
3.48-3.60.17231370.16052657X-RAY DIFFRACTION100
3.6-3.750.19251380.15422615X-RAY DIFFRACTION100
3.75-3.920.18131380.13932670X-RAY DIFFRACTION100
3.92-4.130.15111370.13542618X-RAY DIFFRACTION99
4.13-4.380.18151410.13712635X-RAY DIFFRACTION100
4.38-4.720.16631390.13612692X-RAY DIFFRACTION100
4.72-5.20.17011370.1522678X-RAY DIFFRACTION100
5.2-5.950.19681420.17172686X-RAY DIFFRACTION100
5.95-7.480.19361380.17842736X-RAY DIFFRACTION100
7.48-39.850.20121500.18892792X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -45.9308 Å / Origin y: 41.8292 Å / Origin z: 3.2282 Å
111213212223313233
T0.3173 Å2-0.0975 Å2-0.0036 Å2-0.3419 Å2-0.0236 Å2--0.3294 Å2
L0.7085 °2-0.1793 °2-0.145 °2-1.2862 °20.4157 °2--1.0075 °2
S0.0293 Å °0.0253 Å °-0.0204 Å °-0.0029 Å °0.0007 Å °-0.0537 Å °-0.0384 Å °0.0902 Å °-0.0421 Å °
Refinement TLS groupSelection details: all

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