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- PDB-3dr0: Structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002 -

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Basic information

Entry
Database: PDB / ID: 3dr0
TitleStructure of reduced cytochrome c6 from Synechococcus sp. PCC 7002
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / Cytochrome / photosynthesis / cyanobacteria / electron transfer / Heme / Iron / Metal-binding / Thylakoid / Transport
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-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c6
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsBialek, W. / Krzywda, S. / Jaskolski, M. / Szczepaniak, A.
Citation
Journal: Febs J. / Year: 2009
Title: Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion
Authors: Bialek, W. / Krzywda, S. / Jaskolski, M. / Szczepaniak, A.
#1: Journal: Biochemistry / Year: 2008
Title: Deeply branching c6-like cytochromes of cyanobacteria
Authors: Bialek, W. / Nelson, M. / Tamiola, K. / Kallas, T. / Szczepaniak, A.
#2: Journal: The Phototrophic Prokaryotes / Year: 1999
Title: Cytochrome c6 from Synechococcus sp. PCC 7002
Authors: Nomura, C. / Bryant, D.A.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,3818
Polymers28,3393
Non-polymers2,0425
Water9,422523
1
A: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0632
Polymers9,4461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2554
Polymers9,4461
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0632
Polymers9,4461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.879, 82.879, 28.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 9446.432 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: co-expression with pEC86 / Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Gene: petJ / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: O30881
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10mM HEPES, 2.2M Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.817 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 21, 2006 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.817 Å / Relative weight: 1
ReflectionResolution: 1.22→71.8 Å / Num. all: 62938 / Num. obs: 62908 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 25.3
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.4 / % possible all: 73.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0039refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1CTJ

1ctj


Resolution: 1.23→19.58 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.302 / SU ML: 0.026 / Isotropic thermal model: Anisotropic ADPs / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13771 1274 2 %RANDOM
Rwork0.10709 ---
obs0.10771 61634 98.75 %-
all-62938 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.23→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 139 523 2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222289
X-RAY DIFFRACTIONr_bond_other_d0.0010.021375
X-RAY DIFFRACTIONr_angle_refined_deg1.6872.1093135
X-RAY DIFFRACTIONr_angle_other_deg1.6333.0043370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28926.56296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.982153
X-RAY DIFFRACTIONr_chiral_restr0.1060.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6191.51402
X-RAY DIFFRACTIONr_mcbond_other0.5781.5582
X-RAY DIFFRACTIONr_mcangle_it2.26922186
X-RAY DIFFRACTIONr_scbond_it3.3153887
X-RAY DIFFRACTIONr_scangle_it4.3064.5949
X-RAY DIFFRACTIONr_rigid_bond_restr1.41813664
X-RAY DIFFRACTIONr_sphericity_free12.6675523
X-RAY DIFFRACTIONr_sphericity_bonded4.40753597
LS refinement shellResolution: 1.226→1.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 89 -
Rwork0.237 3963 -
obs--85.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90430.4475-0.07282.96460.55723.5448-0.03970.0880.0822-0.0978-0.0124-0.0695-0.18010.04890.05220.07910.0122-0.01640.0679-0.0110.099930.3078-18.0786-7.9964
21.2156-0.21790.07981.26530.10181.329-0.0174-0.0145-0.11930.02390.0190.02370.0827-0.0273-0.00160.0643-0.0080.00680.05760.00480.075426.3122-32.0445-10.1208
34.8728-2.6969-0.66442.95240.82870.8024-0.0777-0.01060.0801-0.00440.0324-0.036-0.05120.01360.04530.0507-0.0027-0.0130.02240.00120.029230.4577-22.508-12.5056
42.7036-0.75790.55892.2036-0.38114.9799-0.0754-0.09390.11520.0598-0.03140.0004-0.2278-0.03970.10670.0662-0.0062-0.00190.06110.01290.092510.45487.0679-2.0158
50.98150.02910.061.3109-0.10271.0202-0.00080.00740.01280.0008-0.0156-0.0826-0.01180.08540.01640.05510.00840.00140.06920.00640.051914.1377-3.41941.1614
61.5831-0.8684-0.61062.00520.76470.60020.05850.06970.0757-0.0958-0.0535-0.0302-0.0406-0.0401-0.00490.0595-0.00290.0020.06880.01020.070330.626121.4571-14.0271
71.60360.0933-0.00152.27770.99432.50050.00140.0336-0.00970.0043-0.04330.12670.0288-0.15540.04190.0393-0.0071-0.00510.05110.0070.056922.419716.3696-9.1192
82.03232.08660.05416.69570.61870.6696-0.0445-0.03-0.01220.0220.0329-0.10930.02090.02720.01150.04730.01050.00880.0540.00250.054534.273217.2052-7.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 161 - 16
2X-RAY DIFFRACTION2AA17 - 7017 - 70
3X-RAY DIFFRACTION3AA71 - 9371 - 93
4X-RAY DIFFRACTION4BB1 - 161 - 16
5X-RAY DIFFRACTION5BB17 - 9317 - 93
6X-RAY DIFFRACTION6CC1 - 401 - 40
7X-RAY DIFFRACTION7CC41 - 7241 - 72
8X-RAY DIFFRACTION8CC73 - 9373 - 93

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