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Yorodumi- PDB-3un1: Crystal structure of an oxidoreductase from Sinorhizobium melilot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3un1 | ||||||
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Title | Crystal structure of an oxidoreductase from Sinorhizobium meliloti 1021 | ||||||
Components | Probable oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 an oxidoreductase 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 | 3un1.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3un1.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 3un1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3un1_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 3un1_full_validation.pdf.gz | 494.5 KB | Display | |
Data in XML | 3un1_validation.xml.gz | 37 KB | Display | |
Data in CIF | 3un1_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/3un1 ftp://data.pdbj.org/pub/pdb/validation_reports/un/3un1 | HTTPS FTP |
-Related structure data
Related structure data | 3d3wS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28581.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: y20210, RB0203, SM_b20210 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL References: UniProt: Q9EXU6, UniProt: Q7ANT0*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 30% (v/v) PEG550MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 38775 / Num. obs: 38775 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4 / Num. unique all: 3804 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D3W Resolution: 2.45→47.38 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.596 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.442 / ESU R Free: 0.266 / 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: 34.217 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→47.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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