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- PDB-6u97: Structure of OmcF_H47I mutant -

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Basic information

Entry
Database: PDB / ID: 6u97
TitleStructure of OmcF_H47I mutant
ComponentsLipoprotein cytochrome c, 1 heme-binding site
KeywordsELECTRON TRANSPORT / OmcF / redox-Bohr effect
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 / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsPokkuluri, P.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Front Microbiol / Year: 2019
Title: Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF FromGeobacter sulfurreducens.
Authors: Teixeira, L.R. / Cordas, C.M. / Fonseca, M.P. / Duke, N.E.C. / Pokkuluri, P.R. / Salgueiro, C.A.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein cytochrome c, 1 heme-binding site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1403
Polymers8,4281
Non-polymers7132
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.186, 39.019, 49.218
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 Lipoprotein cytochrome c, 1 heme-binding site


Mass: 8427.596 Da / Num. of mol.: 1 / Mutation: H47I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA / Gene: omcF, GSU2432 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74AE4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.44 % / Description: needle clusters
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 0.1 M Hepes pH 7.5, 2% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 31673 / % possible obs: 99 % / Redundancy: 11 % / Biso Wilson estimate: 10.02 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Χ2: 0.929 / Net I/σ(I): 42.5
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1901 / CC1/2: 0.963 / Rpim(I) all: 0.114 / Rrim(I) all: 0.327 / Χ2: 0.958 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→23.87 Å / SU ML: 0.0605 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 19.3043
RfactorNum. reflection% reflection
Rfree0.1528 897 4.93 %
Rwork0.1263 --
obs0.1275 18212 64.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.97 Å2
Refinement stepCycle: LAST / Resolution: 1.13→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 5 92 719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137665
X-RAY DIFFRACTIONf_angle_d1.2754925
X-RAY DIFFRACTIONf_chiral_restr0.088292
X-RAY DIFFRACTIONf_plane_restr0.0121120
X-RAY DIFFRACTIONf_dihedral_angle_d15.5125354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.20.2189290.1672555X-RAY DIFFRACTION12.69
1.2-1.290.1362730.09251385X-RAY DIFFRACTION31.43
1.29-1.420.13311460.08682789X-RAY DIFFRACTION63.24
1.42-1.630.12421850.08753691X-RAY DIFFRACTION82.98
1.63-2.050.1312350.124269X-RAY DIFFRACTION95.59
2.05-23.870.1712290.14214626X-RAY DIFFRACTION99.06

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