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- PDB-2hpv: Crystal structure of FMN-Dependent azoreductase from Enterococcus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hpv | ||||||
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Title | Crystal structure of FMN-Dependent azoreductase from Enterococcus faecalis | ||||||
![]() | FMN-dependent NADH-azoreductase | ||||||
![]() | OXIDOREDUCTASE / Azoreductase / Enterococcus faecalis / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | ![]() FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on other nitrogenous compounds as donors / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Z.J. / Chen, L. / Chen, H. / Rose, J. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.1 KB | Display | ![]() |
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PDB format | ![]() | 151.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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