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Yorodumi- PDB-1jry: Crystal structure of Arg402Lys mutant flavocytochrome c3 from She... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jry | |||||||||
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Title | Crystal structure of Arg402Lys mutant flavocytochrome c3 from Shewanella frigidimarina | |||||||||
Components | FLAVOCYTOCHROME C | |||||||||
Keywords | OXIDOREDUCTASE / fumarate reductase / mutant / flavocytochrome | |||||||||
Function / homology | Function and homology information fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Shewanella frigidimarina (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Mowat, C.G. / Moysey, R. / Miles, C.S. / Leys, D. / Doherty, M.K. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase. Authors: Mowat, C.G. / Moysey, R. / Miles, C.S. / Leys, D. / Doherty, M.K. / 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 | 1jry.cif.gz | 282.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jry.ent.gz | 220.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jry_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1jry_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1jry_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 1jry_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jry ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jry | HTTPS FTP |
-Related structure data
Related structure data | 1jrxC 1jrzC 1qjdS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60599.227 Da / Num. of mol.: 2 / Mutation: R402K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: fcc / Plasmid: pMMB503EH / Species (production host): Shewanella frigidimarina Production host: Shewanella frigidimarina NCIMB 400 (bacteria) Strain (production host): NCIMB400 References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 5 types, 1856 molecules
#2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, TrisHCl, sodium chloride, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
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: PX14.2 / Wavelength: 1.244 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2000 |
Radiation | Monochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 79505 / Num. obs: 79425 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.286 / Num. unique all: 79425 |
Reflection | *PLUS Num. measured all: 538082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJD Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 13 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.1624 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 2.7 |