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Yorodumi- PDB-1vyp: Structure of pentaerythritol tetranitrate reductase W102F mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vyp | ||||||
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Title | Structure of pentaerythritol tetranitrate reductase W102F mutant and 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: 1.27 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: Crystallization and Preliminary Diffraction Studies of Pentaerythritol Tetranitrate 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 "XB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XB" 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 | 1vyp.cif.gz | 178.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vyp.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/1vyp ftp://data.pdbj.org/pub/pdb/validation_reports/vy/1vyp | HTTPS FTP |
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-Related structure data
Related structure data | 1vyrC 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: 39364.965 Da / Num. of mol.: 1 / Mutation: YES 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 / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % |
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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, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→50 Å / Num. obs: 29340 / % possible obs: 93.8 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.27→1.32 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.5 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GVS Resolution: 1.27→37.8 Å / SU B: 0.549 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042
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Displacement parameters | Biso mean: 9.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→37.8 Å
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