+Open data
-Basic information
Entry | Database: PDB / ID: 4la4 | ||||||
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Title | Crystal structure of native PnpB | ||||||
Components | NAD(P)H dehydrogenase (quinone)NAD(P)H dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE / native PnpB / para-benzoquinone reductase | ||||||
Function / homology | Function and homology information p-benzoquinone reductase (NADPH) / p-benzoquinone reductase (NADPH) activity / 4-nitrophenol catabolic process / NAD(P)H dehydrogenase (quinone) activity / : / NAD binding / FMN binding / flavin adenine dinucleotide binding / NADP binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Su, J. / Zhang, C. / Li, N. / Gu, L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of native PnpB Authors: Su, J. / Zhang, C. / Li, N. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4la4.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4la4.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 4la4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4la4 ftp://data.pdbj.org/pub/pdb/validation_reports/la/4la4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22061.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: WBC-3 / Gene: pnpB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C1I202, NAD(P)H dehydrogenase (quinone) #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: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2010 | |||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.07→50 Å / Num. all: 22471 / Num. obs: 22471 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→40.116 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.868 / SU ML: 0.2 / σ(F): 0 / Phase error: 19.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.024 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.95 Å2 / Biso mean: 31.8854 Å2 / Biso min: 14.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→40.116 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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