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- PDB-1gvs: Structure of pentaerythritol tetranitrate reductase and complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gvs | ||||||
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Title | Structure of pentaerythritol tetranitrate reductase and complexed with picric acid | ||||||
![]() | PENTAERYTHRITOL TETRANITRATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / EXPLOSIVE DEGRADATION / STEROID BINDING | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barna, T. / Moody, P.C.E. | ||||||
![]() | ![]() Title: Kinetic and Structural Basis of Reactivity of Pentaerythritol Tetranitrate Reductase with Nadph,2-Cyclohexenone Nitroesters and Nitroaromatic Explosives Authors: Khan, H. / Harris, R. / Barna, T. / Craig, D. / Bruce, N. / Munro, A. / Moody, P.C.E. / Scrutton, N. #1: ![]() 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 "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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 72 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gvoC ![]() 1gvqC ![]() 1gvrC ![]() 1h50S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 Source method: isolated from a genetically manipulated source Details: 2,4,6 TRINITROPHENOL IS BOUND IN THE ACTIVE SITE / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-TNF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.20 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Barna, T.M., (2001) J. Mol. Biol., 310, 433. / pH: 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 68596 / % possible obs: 96.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.38→1.47 Å / % possible all: 79 |
Reflection | *PLUS Highest resolution: 1.55 Å / Num. obs: 48899 / % possible obs: 95.8 % / Num. measured all: 231227 / Rmerge(I) obs: 0.032 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H50 Resolution: 1.38→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.38→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.47 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.55 Å / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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