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Yorodumi- PDB-3ezl: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ezl | ||||||
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Title | Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b | ||||||
Components | Acetoacetyl-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / ACETOACETYL-COA REDUCTASE / BURKHOLDERIA PSEUDOMALLEI / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei 1710b (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ezl.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ezl.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ezl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ezl_validation.pdf.gz | 646.8 KB | Display | wwPDB validaton report |
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Full document | 3ezl_full_validation.pdf.gz | 648.6 KB | Display | |
Data in XML | 3ezl_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 3ezl_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/3ezl ftp://data.pdbj.org/pub/pdb/validation_reports/ez/3ezl | HTTPS FTP |
-Related structure data
Related structure data | 1i01S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27798.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria) Strain: 1710B / Gene: phbB-1, BURPS1710b_2329 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JRS9, acetoacetyl-CoA reductase |
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#2: Chemical | ChemComp-P4C / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PROPLEX-96 A-1: 100MM HEPES PH 7.5, 20% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 12901 / Num. obs: 12901 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 32.87 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 |
Reflection shell | Resolution: 2.25→2.31 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.9 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1i01 modified with ccp4 chainsaw Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.492 / SU ML: 0.158 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.227 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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