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Yorodumi- PDB-3bm2: Crystal structure of a minimal nitroreductase ydjA from Escherich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bm2 | ||||||
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Title | Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor | ||||||
Components | Protein ydjA | ||||||
Keywords | OXIDOREDUCTASE / ydja / nitroreductase | ||||||
Function / homology | Function and homology information Oxidoreductases / FMN binding / oxidoreductase activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Choi, J.W. / Kim, J.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor Authors: Choi, J.-W. / Lee, J. / Nishi, K. / Kim, Y.-S. / Jung, C.-H. / Kim, J.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bm2.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bm2.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bm2_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 3bm2_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 3bm2_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 3bm2_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/3bm2 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/3bm2 | HTTPS FTP |
-Related 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: 20686.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ydjA / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0ACY1, 6,7-dihydropteridine reductase #2: 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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20%(w/v) polyethyleneglycol 1000, 0.2M lithium sulfate, 0.1M phosphate-citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2007 / Details: mirrors |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 26993 / Num. obs: 26237 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.097 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Num. unique all: 2244 / Rsym value: 0.505 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→38.44 Å / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→38.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.12 Å /
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