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Yorodumi- PDB-4dry: The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dry | ||||||
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Title | The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Rhizobium meliloti | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase | ||||||
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 / SAD / Resolution: 2.5 Å | ||||||
Authors | Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / 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: The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Rhizobium meliloti Authors: Zhang, Z. / 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 | 4dry.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dry.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dry_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 4dry_full_validation.pdf.gz | 482.8 KB | Display | |
Data in XML | 4dry_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 4dry_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/4dry ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4dry | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29808.947 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RB1369, SM_b20662 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q92TX5, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | ChemComp-SO4 / #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: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M Ammonium Sulfate, 0.1 M MES monohydrate pH 6.5 10% v/v 1,4-Dixane, 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: 0.9787 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 35258 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 8.6 / Num. unique all: 3489 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→49.064 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 24.83 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.048 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→49.064 Å
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Refine LS restraints |
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LS refinement shell |
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