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- PDB-3cu4: OmcF, Outer membrance cytochrome F from Geobacter sulfurreducens -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3cu4
TitleOmcF, Outer membrance cytochrome F from Geobacter sulfurreducens
ComponentsCytochrome c family protein
KeywordsELECTRON TRANSPORT / cytochrome c6 / Geobacter sulfurreducens / monoheme cytochrome
Function / homology
Function and homology information


plasma membrane-derived thylakoid lumen / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Lipoprotein cytochrome c, 1 heme-binding site
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsPokkuluri, P.R. / Schiffer, M.
CitationJournal: Proteins / Year: 2008
Title: Outer membrane cytochrome c, OmcF, from Geobacter sulfurreducens: High structural similarity to an algal cytochrome c(6).
Authors: Pokkuluri, P.R. / Londer, Y.Y. / Wood, S.J. / Duke, N.E. / Morgado, L. / Salgueiro, C.A. / Schiffer, M.
History
DepositionApr 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2862
Polymers8,6701
Non-polymers6161
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.080, 40.190, 48.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c family protein


Mass: 8669.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU2432 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21 (DE3) cotransformed with plasmid pEC86
References: UniProt: Q74AE4
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 1.2 M trisodium citrate, 0.1 M Tris pH 8.5 (Salt Rx screen-22), microseeding, pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 33541 / Num. obs: 33541 / % possible obs: 96 % / Redundancy: 4.2 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 42.4
Reflection shellResolution: 1.3→1.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 9.7 / Num. unique all: 617 / % possible all: 70

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→24.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 134653.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE FOLLOWING SIDE CHAIN ATOMS HAVE WEAK DENSITY AND ARE PROBABLY DISORDERED: HIS47:CD2,ND1,CE1,NE2 GLU49:CD,OE1,OE2 ARG56:NE,CZ,NH1,NH2 LYS94:CE,NZ GLU97:CD,OE1,OE2
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3243 9.7 %RANDOM
Rwork0.169 ---
obs0.169 33541 94.8 %-
all-33541 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2274 Å2 / ksol: 0.413536 e/Å3
Displacement parametersBiso mean: 11 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.02 Å
Refinement stepCycle: LAST / Resolution: 1.3→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms579 0 43 116 738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.18 461 10.3 %
Rwork0.176 4007 -
obs-4007 76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem.paramhem.top

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