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- PDB-9krc: CRYSTAL STRUCTURE OF OXIDIIZED CYTOCHROME C6 FROM SYNECHOCOCCUS E... -

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Basic information

Entry
Database: PDB / ID: 9krc
TitleCRYSTAL STRUCTURE OF OXIDIIZED CYTOCHROME C6 FROM SYNECHOCOCCUS ELONGATUS PCC 7942
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / CYTOCHROME-C6 / OXIDIIZED STATE
Function / homology
Function and homology information


plasma membrane-derived thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c6
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, B.T. / Liu, S.W. / Xu, Y.C. / Sheng, W. / Gong, Y. / Cao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070259 China
CitationJournal: Int J Mol Sci / Year: 2025
Title: A High-Resolution Crystallographic Study of Cytochrome c6: Structural Basis for Electron Transfer in Cyanobacterial Photosynthesis.
Authors: Zhang, B. / Xu, Y. / Liu, S. / Chen, S. / Zhao, W. / Li, Z. / Wang, J. / Zhao, W. / Zhang, H. / Dong, Y. / Gong, Y. / Sheng, W. / Cao, P.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c6
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7377
Polymers18,2122
Non-polymers1,5255
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-85 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.424, 53.453, 65.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cytochrome c6 / Cytochrome c-553 / Cytochrome c553 / Soluble cytochrome f


Mass: 9106.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: petJ, cytA, Synpcc7942_1630 / Production host: Escherichia coli (E. coli) / References: UniProt: P25935
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M di-Ammonium tartrate, 2.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 35713 / % possible obs: 99.2 % / Redundancy: 2 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.02 / Net I/σ(I): 21.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3257 / CC1/2: 0.977 / Rpim(I) all: 0.104 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.52 Å / SU ML: 0.1119 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.8269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1703 1508 4.22 %
Rwork0.1445 34205 -
obs0.1456 35713 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 101 313 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831420
X-RAY DIFFRACTIONf_angle_d0.95731957
X-RAY DIFFRACTIONf_chiral_restr0.0619198
X-RAY DIFFRACTIONf_plane_restr0.0102252
X-RAY DIFFRACTIONf_dihedral_angle_d14.3623475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.16371280.12523007X-RAY DIFFRACTION97.51
1.45-1.50.18671400.12723064X-RAY DIFFRACTION99.97
1.5-1.560.16071380.13513043X-RAY DIFFRACTION99.97
1.56-1.630.18411320.1243099X-RAY DIFFRACTION100
1.63-1.710.14741340.12243075X-RAY DIFFRACTION99.94
1.71-1.820.16471370.13463086X-RAY DIFFRACTION99.97
1.82-1.960.16231420.14193101X-RAY DIFFRACTION100
1.96-2.160.16331340.13543126X-RAY DIFFRACTION100
2.16-2.470.16281400.14243127X-RAY DIFFRACTION99.94
2.47-3.110.15981400.1633159X-RAY DIFFRACTION100
3.11-41.520.19121430.15423318X-RAY DIFFRACTION99.97

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