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Yorodumi- PDB-2v9c: X-ray Crystallographic Structure of a Pseudomonas aeruginosa Azor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v9c | ||||||
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Title | X-ray Crystallographic Structure of a Pseudomonas aeruginosa Azoreductase in Complex with Methyl Red. | ||||||
Components | FMN-DEPENDENT NADH-AZOREDUCTASE 1 | ||||||
Keywords | OXIDOREDUCTASE / FMN / NAD / FLAVODOXIN / FLAVOPROTEIN / NADPH-DEPENDENT / FLAVIN MONONUCLEOTIDE | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / NADPH:quinone reductase activity / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Wang, C.-J. / Hagemeier, C. / Rahman, N. / Lowe, E.D. / Noble, M.E.M. / Coughtrie, M. / Sim, E. / Westwood, I.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular Cloning, Characterisation and Ligand- Bound Structure of an Azoreductase from Pseudomonas Aeruginosa Authors: Wang, C.-J. / Hagemeier, C. / Rahman, N. / Lowe, E.D. / Noble, M.E.M. / Coughtrie, M. / Sim, E. / Westwood, I.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v9c.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9c.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 2v9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v9c_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2v9c_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2v9c_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2v9c_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9c ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.2818, -0.7354, 0.6163), Vector: |
-Components
#1: Protein | Mass: 23359.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FMN AND METHYL RED COMPLEX / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9I5F3, EC: 1.7.1.6 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 2-((4-(DIMETHYLAM | |
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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: 2.27 Å3/Da / Density % sol: 45.4 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 1.6 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→34 Å / Num. obs: 20681 / % possible obs: 97.4 % / Observed criterion σ(I): 1.6 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.18→2.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1V4B AND 1T5B Resolution: 2.18→34 Å / Stereochemistry target values: ML Details: RESIDUES -2 - 1 ARE DISORDERED. RESIDUES 125 - 126 AND 187 - 192 OF CHAIN A ARE DISORDERED. RESIDUES 123 - 128 AND 187 - 198 OF CHAIN B ARE DISORDERED. REFMAC VERSION 5.3.0037 WAS USED FOR ...Details: RESIDUES -2 - 1 ARE DISORDERED. RESIDUES 125 - 126 AND 187 - 192 OF CHAIN A ARE DISORDERED. RESIDUES 123 - 128 AND 187 - 198 OF CHAIN B ARE DISORDERED. REFMAC VERSION 5.3.0037 WAS USED FOR REFINEMENT EXCEPT FOR THE FINAL REFINEMENT STEP, FOR WHICH PHENIX.REFINE WAS USED.
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Refinement step | Cycle: LAST / Resolution: 2.18→34 Å
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