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Yorodumi- PDB-6gi9: Crystal structure of pentaerythritol tetranitrate reductase (PETN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gi9 | ||||||||||||
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Title | Crystal structure of pentaerythritol tetranitrate reductase (PETNR) mutant I107L | ||||||||||||
Components | Pentaerythritol tetranitrate reductase | ||||||||||||
Keywords | FLAVOPROTEIN / Mutant I107L | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Levy, C.W. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. Authors: Iorgu, A.I. / Baxter, N.J. / Cliff, M.J. / Levy, C. / Waltho, J.P. / Hay, S. / 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 | 6gi9.cif.gz | 275.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gi9.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gi9_validation.pdf.gz | 779 KB | Display | wwPDB validaton report |
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Full document | 6gi9_full_validation.pdf.gz | 780 KB | Display | |
Data in XML | 6gi9_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6gi9_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6gi9 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6gi9 | HTTPS FTP |
-Related structure data
Related structure data | 6gi7C 6gi8C 6giaC 2abaS 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: 40640.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: onr / Production host: Escherichia coli (E. coli) / References: UniProt: P71278 |
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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: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25 % (w/v) PEG 3000, 17 % (v/v) isopropanol, 0.1 M trisodium citrate, 0.1 M cacodylic acid (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.54 Å / Num. obs: 63458 / % possible obs: 98.68 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0633 / Rpim(I) all: 0.0378 / Rrim(I) all: 0.074 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 1.45→1.502 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 6292 / CC1/2: 0.728 / Rpim(I) all: 0.37 / Rrim(I) all: 0.713 / % possible all: 99.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ABA Resolution: 1.45→37.54 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1287
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→37.54 Å
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Refine LS restraints |
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LS refinement shell |
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