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Yorodumi- PDB-3q62: Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q62 | ||||||
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Title | Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis | ||||||
Components | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | ||||||
Keywords | LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold / hotdog fold | ||||||
Function / homology | Function and homology information trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Yersinia pseudotuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Zhang, R. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis Authors: Zhang, R. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q62.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q62.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 3q62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q62 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q62 | HTTPS FTP |
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-Related structure data
Related structure data | 1mkbS S: Starting model for refinement |
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Similar structure data | |
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: 19104.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: CO92 / Gene: fabA, YPTB1450 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q66CF3, EC: 4.2.1.60 #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: 1.86 Å3/Da / Density % sol: 33.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M MES pH 6.0, 1.0M K/Na Tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 15, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 57207 / Num. obs: 57207 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 13.08 Å2 / Rsym value: 0.071 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2731 / Rsym value: 0.669 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MKB Resolution: 1.4→26.185 Å / SU ML: 0.17 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.173 Å2 / ksol: 0.395 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→26.185 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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