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Yorodumi- PDB-1e39: Flavocytochrome C3 from Shewanella frigidimarina histidine 365 mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+39 | |||||||||
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Title | Flavocytochrome C3 from Shewanella frigidimarina histidine 365 mutated to alanine | |||||||||
Components | FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT | |||||||||
Keywords | OXIDOREDUCTASE / FUMARATE REDUCTASE MUTANT H365A / RESPIRATORY FUMARATE REDUCTASE | |||||||||
Function / homology | Function and homology information fumarate reductase (cytochrome) / 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: 1.8 Å | |||||||||
Authors | Doherty, M.K. / Pealing, S.L. / Miles, C.S. / Moysey, R. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Identification of the Active Site Acid/Base Catalyst in a Bacterial Fumarate Reductase: A Kinetic and Crystallographic Study Authors: Doherty, M.K. / Pealing, S.L. / Miles, C.S. / Moysey, R. / Taylor, P. / 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 | 1e39.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e39.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e39_validation.pdf.gz | 755.8 KB | Display | wwPDB validaton report |
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Full document | 1e39_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 1e39_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1e39_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e39 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e39 | HTTPS FTP |
-Related structure data
Related structure data | 1qjdS S: Starting model for refinement |
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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 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA FRIGIDIMARINA (bacteria) / Strain: NCIMB400 / Production host: SHEWANELLA FRIGIDIMARINA (bacteria) References: UniProt: Q07WU7, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 6 types, 613 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-FUM / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN A ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 54.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.4 Details: HANGING DROP, 50-100MM TRIS-HCL PH 7.4, 80MM NACL, 17-20% PEG 8000, 10MM FUMARATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 9, 1999 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→18 Å / Num. obs: 54314 / % possible obs: 90.7 % / Redundancy: 2.699 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.01 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7.14 / % possible all: 74.9 |
Reflection | *PLUS Lowest resolution: 24 Å / Num. measured all: 265858 |
Reflection shell | *PLUS Highest resolution: 1.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QJD Resolution: 1.8→18 Å / Num. parameters: 20251 / Num. restraintsaints: 18150 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5062 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→18 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.247 / Rfactor Rwork: 0.1814 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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