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Yorodumi- PDB-3p67: T26S mutant of pentaerythritol tetranitrate reductase containing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p67 | ||||||
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Title | T26S mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule | ||||||
Components | Pentaerythritol tetranitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / old yellow enzyme family / alpha / beta barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Toogood, H.S. / Scrutton, N.S. | ||||||
Citation | Journal: Chembiochem / Year: 2010 Title: Focused Directed Evolution of Pentaerythritol Tetranitrate Reductase by Using Automated Anaerobic Kinetic Screening of Site-Saturated Libraries Authors: Hulley, M.E. / Toogood, H.S. / Fryszkowska, A. / Mansell, D. / Stephens, G.M. / Gardiner, J.M. / 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 | 3p67.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p67.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 3p67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p67_validation.pdf.gz | 761.3 KB | Display | wwPDB validaton report |
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Full document | 3p67_full_validation.pdf.gz | 761.4 KB | Display | |
Data in XML | 3p67_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 3p67_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/3p67 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/3p67 | HTTPS FTP |
-Related structure data
Related structure data | 3p62C 1h50S 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: 40626.332 Da / Num. of mol.: 1 / Mutation: T26S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr, PETNR / Plasmid: pBluescript II-KS(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, NADPH dehydrogenase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-ACT / |
#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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic blue optics - mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→54.554 Å / Num. all: 56705 / Num. obs: 56705 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 19.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H50 Resolution: 1.5→16.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1547 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9132 / SU B: 2.12 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0895 / SU Rfree: 0.0668 / Cross valid method: THROUGHOUT / ESU R Free: 0.067 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.5 Å2 / Biso mean: 14.5332 Å2 / Biso min: 5.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→16.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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