[English] 日本語
Yorodumi- PDB-3kft: Crystal structure of Pentaerythritol Tetranitrate Reductase compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kft | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Pentaerythritol Tetranitrate Reductase complex with 1,4,5,6-tetrahydro NADH | ||||||
Components | Pentaerythritol tetranitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / NADH:flavin oxidoreductase / NADH oxidase family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pudney, C.R. / Levy, C.W. / Leys, D. / Scrutton, N.S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction. Authors: Pudney, C.R. / Hay, S. / Levy, C. / Pang, J. / Sutcliffe, M.J. / Leys, D. / Scrutton, N.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kft.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kft.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kft_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3kft_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3kft_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 3kft_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kft ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kft | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39404.000 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.95 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M Magnesium chloride, 0.1M Tris HCl pH 8.5 & 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0698 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0698 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 43135 / Num. obs: 43135 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.69 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.77 / Num. unique all: 6646 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.112 Å / SU ML: 0.27 / σ(F): 1.99 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.641 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.112 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|