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Yorodumi- PDB-4jiq: Crystal structure of glycerol trinitrate reductase NerA from Agro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jiq | ||||||
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Title | Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 1-nitro-2-phenylpropene | ||||||
Components | GTN Reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM-Barrel / ene-reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Oberdorfer, G. / Gruber, K. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: The Structure of Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter Reveals the Molecular Reason for Nitro- and Ene-Reductase Activity in OYE Homologues. Authors: Oberdorfer, G. / Binter, A. / Wallner, S. / Durchschein, K. / Hall, M. / Faber, K. / Macheroux, P. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jiq.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jiq.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/4jiq ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jiq | HTTPS FTP |
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-Related structure data
Related structure data | 4jicSC 4jipC 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
#1: Protein | Mass: 40567.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: nerA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31246 | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | ChemComp-1L5 / [( | ||
#4: Chemical | #5: 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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v polyethylene glycol 3,350, pH 6.0, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010 |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→55.69 Å / Num. all: 14144 / Num. obs: 14125 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.49→2.62 Å / Redundancy: 3.5 % / Num. unique all: 2021 / Rsym value: 0.677 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4jic Resolution: 2.49→50.343 Å / SU ML: 0.84 / σ(F): 1.33 / Phase error: 24.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.477 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.49→50.343 Å
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Refine LS restraints |
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LS refinement shell |
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