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Yorodumi- PDB-3tox: Crystal structure of a short chain dehydrogenase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tox | ||||||
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Title | Crystal structure of a short chain dehydrogenase in complex with NAD(P) from Sinorhizobium meliloti 1021 | ||||||
Components | Short chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / short chain dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a short chain dehydrogenase in complex with NAD(P) from Sinorhizobium meliloti 1021 Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tox.cif.gz | 379.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tox.ent.gz | 310.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tox_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 3tox_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 3tox_validation.xml.gz | 84.6 KB | Display | |
Data in CIF | 3tox_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3tox ftp://data.pdbj.org/pub/pdb/validation_reports/to/3tox | HTTPS FTP |
-Related structure data
Related structure data | 1rwdS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28418.943 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00292, SMc00372 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92SS3 #2: Chemical | ChemComp-NAP / #3: 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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 135387 / Num. obs: 135387 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3 / Num. unique all: 13380 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1RWD Resolution: 1.93→43.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.862 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.181 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.258 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→43.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.934→1.984 Å / Total num. of bins used: 20
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