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Yorodumi- PDB-2hpv: Crystal structure of FMN-Dependent azoreductase from Enterococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hpv | ||||||
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Title | Crystal structure of FMN-Dependent azoreductase from Enterococcus faecalis | ||||||
Components | FMN-dependent NADH-azoreductase | ||||||
Keywords | OXIDOREDUCTASE / Azoreductase / Enterococcus faecalis / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor / oxidoreductase activity, acting on other nitrogenous compounds as donors / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Liu, Z.J. / Chen, L. / Chen, H. / Rose, J. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Fmn-Dependent Azoreductase from Enterococcus faecalis at 2.00 A resolution Authors: Liu, Z.J. / Chen, H. / Chen, L. / Shah, N. / Rose, J.P. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hpv.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hpv.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/2hpv ftp://data.pdbj.org/pub/pdb/validation_reports/hp/2hpv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: SER / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 2 - 208 / Label seq-ID: 2 - 208
NCS ensembles :
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-Components
#1: Protein | Mass: 23432.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: azoR, azoA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: Q831B2, Oxidoreductases; Acting on other nitrogenous compounds as donors #2: Chemical | ChemComp-FMN / #3: 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: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.09M HEPES/NAOH ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.09M HEPES/NAOH BUFFER, 1.26M TRI-SODIUM CITRATE DIHYDRATE, 10% V/V GLYCEROL, pH 7.5, temperature 293K |
-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2005 / Details: ROSENBAUM |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.8 Å / Num. obs: 64925 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rsym value: 0.07 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.7 % / Num. unique all: 5096 / Rsym value: 0.457 / % possible all: 65.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→25.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.093 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.182 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.789 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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