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- PDB-9krd: CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM SYNECHOCOCCUS ELO... -

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Basic information

Entry
Database: PDB / ID: 9krd
TitleCRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM SYNECHOCOCCUS ELONGATUS PCC 7942
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / CYTOCHROME-C6 / REDUCED STATE / PHOTOSYNTHESIS
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: 1.7 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,18611
Polymers36,4244
Non-polymers2,7627
Water8,791488
1
A: Cytochrome c6
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6416
Polymers18,2122
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-71 kcal/mol
Surface area8870 Å2
MethodPISA
2
B: Cytochrome c6
C: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5455
Polymers18,2122
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-60 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.505, 73.873, 98.781
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.: 4
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.: 4 / 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.: 488 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Citric acid pH 4.0, 1.6M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 43231 / % possible obs: 96.9 % / Redundancy: 10 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.016 / Net I/σ(I): 29.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 3670 / CC1/2: 0.986 / Rpim(I) all: 0.085 / Χ2: 0.986 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.25 Å / SU ML: 0.1797 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1871 2167 5.03 %
Rwork0.1673 40902 -
obs0.1683 43069 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 187 488 3204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792795
X-RAY DIFFRACTIONf_angle_d0.89433847
X-RAY DIFFRACTIONf_chiral_restr0.0389391
X-RAY DIFFRACTIONf_plane_restr0.0094495
X-RAY DIFFRACTIONf_dihedral_angle_d14.9452937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25821250.22442187X-RAY DIFFRACTION79.18
1.74-1.780.22041400.19652541X-RAY DIFFRACTION92.04
1.78-1.830.2261330.17552775X-RAY DIFFRACTION98.14
1.83-1.890.20731410.16422745X-RAY DIFFRACTION98.53
1.89-1.950.2031430.16772781X-RAY DIFFRACTION99.12
1.95-2.020.20591850.17432737X-RAY DIFFRACTION99.29
2.02-2.10.21331370.1732768X-RAY DIFFRACTION98.98
2.1-2.190.18741310.17242798X-RAY DIFFRACTION99.46
2.19-2.310.1881460.16122796X-RAY DIFFRACTION99.53
2.31-2.450.1651390.16072825X-RAY DIFFRACTION99.7
2.45-2.640.18651370.17242822X-RAY DIFFRACTION99.6
2.64-2.910.20041570.17022818X-RAY DIFFRACTION99.73
2.91-3.330.22111680.18252830X-RAY DIFFRACTION99.73
3.33-4.190.1611280.1492476X-RAY DIFFRACTION85.43
4.19-27.250.14641570.15633003X-RAY DIFFRACTION99.56

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