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- PDB-9krr: CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM Synechocystis PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 9krr
TitleCRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM Synechocystis PCC 6803
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 / IODIDE ION / Cytochrome c6
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 28, 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
E: Cytochrome c6
F: Cytochrome c6
G: Cytochrome c6
H: Cytochrome c6
I: Cytochrome c6
J: Cytochrome c6
K: Cytochrome c6
L: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,86064
Polymers106,10212
Non-polymers11,75852
Water23,1131283
1
A: Cytochrome c6
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,90913
Polymers17,6842
Non-polymers2,22511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytochrome c6
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,55910
Polymers17,6842
Non-polymers1,8758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cytochrome c6
F: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,87813
Polymers17,6842
Non-polymers2,19411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Cytochrome c6
H: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,55910
Polymers17,6842
Non-polymers1,8758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Cytochrome c6
J: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,59010
Polymers17,6842
Non-polymers1,9068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Cytochrome c6
L: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3678
Polymers17,6842
Non-polymers1,6836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.899, 74.437, 133.182
Angle α, β, γ (deg.)90.000, 106.111, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 8841.871 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (bacteria)
Gene: petJ, sll1796 / Production host: Escherichia coli (E. coli) / References: UniProt: P46445
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1283 / 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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M Sodium iodide, 2.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.93→70 Å / Num. obs: 105090 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.036 / Net I/σ(I): 12.6
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3 / Num. unique obs: 15145 / CC1/2: 0.845 / Rpim(I) all: 0.262

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→56.39 Å / SU ML: 0.1738 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.876
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 1940 1.9 %
Rwork0.1683 100108 -
obs0.1691 102048 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.04 Å2
Refinement stepCycle: LAST / Resolution: 1.93→56.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7373 0 652 1283 9308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738169
X-RAY DIFFRACTIONf_angle_d0.888211211
X-RAY DIFFRACTIONf_chiral_restr0.04281103
X-RAY DIFFRACTIONf_plane_restr0.00621446
X-RAY DIFFRACTIONf_dihedral_angle_d14.48082731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.26651240.22246421X-RAY DIFFRACTION87.37
1.98-2.040.261350.19736780X-RAY DIFFRACTION92.35
2.04-2.10.25041340.1826870X-RAY DIFFRACTION94.01
2.1-2.160.21891410.17027015X-RAY DIFFRACTION95.69
2.16-2.240.19861370.16747112X-RAY DIFFRACTION96.32
2.24-2.330.2041380.17197125X-RAY DIFFRACTION97.19
2.33-2.440.22741370.17757200X-RAY DIFFRACTION97.83
2.44-2.560.21411400.17967278X-RAY DIFFRACTION98.53
2.56-2.730.23581410.18367288X-RAY DIFFRACTION99.13
2.73-2.940.23351410.1867339X-RAY DIFFRACTION99.39
2.94-3.230.23841440.18557372X-RAY DIFFRACTION99.73
3.23-3.70.19841410.15167389X-RAY DIFFRACTION99.74
3.7-4.660.15711430.13237419X-RAY DIFFRACTION99.76
4.66-56.390.19271440.15967500X-RAY DIFFRACTION98.94

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