+Open data
-Basic information
Entry | Database: PDB / ID: 1p2e | |||||||||
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Title | H61A mutant of flavocytochrome c3 | |||||||||
Components | flavocytochrome c3 | |||||||||
Keywords | OXIDOREDUCTASE / flavocytochrome c3 / fumarate reductase | |||||||||
Function / homology | Function and homology information fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Shewanella frigidimarina (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Rothery, E.L. / Mowat, C.G. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Histidine 61: An Important Heme Ligand in the Soluble Fumarate Reductase from Shewanella frigidimarina Authors: Rothery, E.L. / Mowat, C.G. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p2e.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p2e.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 1p2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p2e_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 1p2e_full_validation.pdf.gz | 796.8 KB | Display | |
Data in XML | 1p2e_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1p2e_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2e ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2e | HTTPS FTP |
-Related structure data
Related structure data | 1p2hC 1qjdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60560.172 Da / Num. of mol.: 1 / Fragment: flavocytochrome c3 fumarate reductase / Mutation: H61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: FCC / Plasmid: pMMB503EH / Production host: Shewanella frigidimarina (bacteria) / Strain (production host): EG301 References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 6 types, 529 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-FUM / | #6: Chemical | ChemComp-ACY / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, TrisHCl, NaCl, sodium fumarate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.992 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→17 Å / Num. all: 29786 / Num. obs: 29268 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.23 / Num. unique all: 2932 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 205404 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1QJD Resolution: 2.2→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2581 / Rfactor Rwork: 0.1751 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |