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Yorodumi- PDB-1ylr: The structure of E.coli nitroreductase with bound acetate, crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ylr | ||||||
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Title | The structure of E.coli nitroreductase with bound acetate, crystal form 1 | ||||||
Components | Oxygen-insensitive NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / Oxygen-insensitive NAD(P)H nitroreductase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Race, P.R. / Lovering, A.L. / Green, R.M. / Ossor, A. / White, S.A. / Searle, P.F. / Wrighton, C.J. / Hyde, E.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme. Authors: Race, P.R. / Lovering, A.L. / Green, R.M. / Ossor, A. / White, S.A. / Searle, P.F. / Wrighton, C.J. / Hyde, E.I. #1: 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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Remark 600 | HETEROGEN LIGANDS 1218-1219 ARE ASSOCIATED WITH CHAIN A. LIGANDS 2218-2219 ARE ASSOCIATED WITH CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ylr.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ylr.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ylr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1ylr ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1ylr | HTTPS FTP |
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-Related structure data
Related structure data | 1ykiC 1yluC 1icrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23937.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfnB, dprA, nfsB, nfsI, ntr / Plasmid: pET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38489, 6,7-dihydropteridine reductase #2: Chemical | #3: Chemical | #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: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→56.25 Å / Num. all: 49614 / Num. obs: 47753 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.107 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 7068 / Rsym value: 0.403 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ICR Resolution: 1.7→56.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.68 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.206 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→56.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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