+Open data
-Basic information
Entry | Database: PDB / ID: 6u97 | ||||||
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Title | Structure of OmcF_H47I mutant | ||||||
Components | Lipoprotein cytochrome c, 1 heme-binding site | ||||||
Keywords | ELECTRON 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 | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||
Authors | Pokkuluri, P.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u97.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u97.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 6u97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u97 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u97 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.44 % / Description: needle clusters |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.8 M ammonium sulfate, 0.1 M Hepes pH 7.5, 2% (v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→23.87 Å
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Refine LS restraints |
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LS refinement shell |
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