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Yorodumi- PDB-4itu: Crystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4itu | ||||||
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Title | Crystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (S-HPCDH) bound to S-HPC AND NADH | ||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold | ||||||
Function / homology | Function and homology information 2-(S)-hydroxypropyl-CoM dehydrogenase / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Xanthobacter autotrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Bakelar, J.W. / Johnson, S.J. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases. Authors: Bakelar, J.W. / Sliwa, D.A. / Johnson, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4itu.cif.gz | 209.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4itu.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 4itu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4itu_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4itu_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4itu_validation.xml.gz | 46 KB | Display | |
Data in CIF | 4itu_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4itu ftp://data.pdbj.org/pub/pdb/validation_reports/it/4itu | HTTPS FTP |
-Related structure data
Related structure data | 4gh5SC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27112.775 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: PY2 / Plasmid: PET28-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7IQH5 #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-1HS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.35 M Ammonium Acetate, 27 % PEG 3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2013 / 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: 1.6→35 Å / Num. all: 108385 / Num. obs: 108385 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7306 / % possible all: 63.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4GH5 Resolution: 1.6→34.649 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.073 Å2 / ksol: 0.43 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→34.649 Å
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Refine LS restraints |
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LS refinement shell |
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