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Yorodumi- PDB-1icv: THE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1icv | ||||||
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Title | THE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH NICOTINIC ACID | ||||||
Components | OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta | ||||||
Function / homology | Function and homology information : / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Lovering, A.L. / Hyde, E.I. / Searle, P.F. / White, S.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The structure of Escherichia coli nitroreductase complexed with nicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution. Authors: Lovering, A.L. / Hyde, E.I. / Searle, P.F. / White, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1icv.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1icv.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 1icv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/1icv ftp://data.pdbj.org/pub/pdb/validation_reports/ic/1icv | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 24171.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NFSB / Plasmid: PET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38489, 1.6.99.7 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-NIO / #4: 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: 2.56 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG8K, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9793, 0.9795, 0.9393 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→19.95 Å / Num. all: 123859 / Num. obs: 39289 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 4.9 / Net I/σ(I): 9.8 | ||||||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 3.2 / Rsym value: 12.3 / % possible all: 98.5 | ||||||||||||
Reflection | *PLUS Num. measured all: 123859 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→100 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.9 Å2 |