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Yorodumi- PDB-1vyr: Structure of pentaerythritol tetranitrate reductase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vyr | ||||||
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Title | Structure of pentaerythritol tetranitrate reductase complexed with picric acid | ||||||
Components | PENTAERYTHRITOL TETRANITRATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / EXPLOSIVE DEGRADATION / STEROID BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ENTEROBACTER CLOACAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | ||||||
Authors | Barna, T. / Moody, P.C.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Atomic Resolution Structures and Solution Behavior of Enzyme-Substrate Complexes of Enterobacter Cloacae Pb2 Pentaerythritol Tetranitrate Reductase: Multiple Conformational States and ...Title: Atomic Resolution Structures and Solution Behavior of Enzyme-Substrate Complexes of Enterobacter Cloacae Pb2 Pentaerythritol Tetranitrate Reductase: Multiple Conformational States and Implications for the Mechanism of Nitroaromatic Explosive Degradation Authors: Khan, H. / Barna, T. / Harris, R. / Bruce, N. / Barsukov, I. / Munro, A. / Moody, P.C.E. / Scrutton, N. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure of Pentaerythritol Tetranitrate Reductase: "Flipped" Binding Geometries for Steroid Substrates in Different Redox States of the Enzyme Authors: Barna, T.M. / Khan, H. / Bruce, N.C. / Barsukov, I. / Scrutton, N.S. / Moody, P.C. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallisation and Preliminary Diffraction Studies of Pentaerythritol Reductase from Enterobacter Cloacae Pb2 Authors: Moody, P.C.E. / Shikotra, N. / French, C.E. / Bruce, N.C. / Scrutton, N.S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vyr.cif.gz | 230.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vyr.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vyr_validation.pdf.gz | 798.9 KB | Display | wwPDB validaton report |
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Full document | 1vyr_full_validation.pdf.gz | 804.3 KB | Display | |
Data in XML | 1vyr_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1vyr_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/1vyr ftp://data.pdbj.org/pub/pdb/validation_reports/vy/1vyr | HTTPS FTP |
-Related structure data
Related structure data | 1vypC 1vysC 1gvsS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 39404.000 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-365 Source method: isolated from a genetically manipulated source Details: 2,4,6 TRINITROPHENOL IS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Description: NCBI U68759. RECOMBINANT / Plasmid: PONR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P71278 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-TNF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | pH: 6.2 / Details: pH 6.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→10 Å / Num. obs: 68596 / % possible obs: 94.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 0.9→0.94 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 65.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GVS Resolution: 0.9→10 Å / Num. parameters: 33636 / Num. restraintsaints: 40616 / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Num. disordered residues: 32 / Occupancy sum hydrogen: 2459.36 / Occupancy sum non hydrogen: 3575.74 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→10 Å
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Refine LS restraints |
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