+Open data
-Basic information
Entry | Database: PDB / ID: 3s6j | ||||||
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Title | The crystal structure of a hydrolase from Pseudomonas syringae | ||||||
Components | Hydrolase, haloacid dehalogenase-like family | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.198 Å | ||||||
Authors | Zhang, Z. / Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a hydrolase from Pseudomonas syringae Authors: Zhang, Z. / Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s6j.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s6j.ent.gz | 215.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s6j_validation.pdf.gz | 486.8 KB | Display | wwPDB validaton report |
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Full document | 3s6j_full_validation.pdf.gz | 517.7 KB | Display | |
Data in XML | 3s6j_validation.xml.gz | 50 KB | Display | |
Data in CIF | 3s6j_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6j ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6j | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26072.820 Da / Num. of mol.: 6 / Fragment: UNP residues 105-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Gene: PSPTO0276, PSPTO_0276 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-coden+RIL(p)-Stratagene / References: UniProt: Q88AV7 #2: Chemical | ChemComp-CA / #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: 1.96 Å3/Da / Density % sol: 37.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Calcium chloride, 0.1 M HEPES, 28% PEG400, 0.1 M EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 59117 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.7 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.198→49.89 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / σ(F): 0.13 / Phase error: 26.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.354 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.198→49.89 Å
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Refine LS restraints |
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LS refinement shell |
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