+Open data
-Basic information
Entry | Database: PDB / ID: 2abb | ||||||
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Title | Structure of PETN reductase Y186F in complex with cyanide | ||||||
Components | pentaerythritol tetranitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / PETN reductase / proton transfer / flavoenzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Khan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: Proton transfer in the oxidative half-reaction of pentaerythritol tetranitrate reductase Authors: Khan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2abb.cif.gz | 178.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2abb.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 2abb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2abb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2abb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2abb_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 2abb_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/2abb ftp://data.pdbj.org/pub/pdb/validation_reports/ab/2abb | HTTPS FTP |
-Related structure data
Related structure data | 2abaC 1vyrS 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: 39388.000 Da / Num. of mol.: 1 / Mutation: Y186F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71278, EC: 1.7.99.- |
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#2: Chemical | ChemComp-SCN / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-IPA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 25%(w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid(pH 6.2), 17%(v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1→15 Å / Num. all: 172733 / Num. obs: 169624 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1→1.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.489 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VYR Resolution: 1→14.37 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.696 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1→14.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20 /
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