+Open data
-Basic information
Entry | Database: PDB / ID: 1h63 | ||||||
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Title | Structure of the reduced Pentaerythritol Tetranitrate Reductase | ||||||
Components | PENTAERYTHRITOL TETRANITRATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / REDUCED FLAVOENZYME | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ENTEROBACTER CLOACAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Barna, T.M. / Moody, P.C.E. | ||||||
Citation | 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. | ||||||
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 | 1h63.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h63.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h63_validation.pdf.gz | 771.2 KB | Display | wwPDB validaton report |
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Full document | 1h63_full_validation.pdf.gz | 775.7 KB | Display | |
Data in XML | 1h63_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1h63_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h63 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h63 | HTTPS FTP |
-Related structure data
Related structure data | 1h50C 1h51C 1h60C 1h61C 1h62C 1oyaS C: citing same article (ref.) S: Starting model for refinement |
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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 Source method: isolated from a genetically manipulated source Details: NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE / Source: (gene. exp.) ENTEROBACTER CLOACAE (bacteria) / Strain: PB2 / Plasmid: PONR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / References: UniProt: P71278 |
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#2: Chemical | ChemComp-FMN / |
#3: 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: 2.17 Å3/Da / Density % sol: 43.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: PEG 4000, 0.1M CACODYLIC ACID, PH 6.8, 12% I-PROPANOL, 0.1M SODIUM CITRATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→100 Å / Num. obs: 44592 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.62→1.68 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.8 / % possible all: 77.3 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 100 Å / Num. obs: 56352 / % possible obs: 96.7 % / Num. measured all: 597225 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS Rmerge(I) obs: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OYA Resolution: 1.62→27.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1468190.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.6084 Å2 / ksol: 0.347313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.62→27.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.72 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor obs: 0.195 / Rfactor Rfree: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 |