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Yorodumi- PDB-4psu: Crystal structure of alpha/beta hydrolase from Rhodopseudomonas p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4psu | ||||||
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Title | Crystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009 | ||||||
Components | Alpha/beta hydrolase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / esterase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Nocek, B. / Hajighasemi, M. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009 Authors: Nocek, B. / Hajighasemi, M. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4psu.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4psu.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 4psu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4psu_validation.pdf.gz | 645.1 KB | Display | wwPDB validaton report |
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Full document | 4psu_full_validation.pdf.gz | 646.5 KB | Display | |
Data in XML | 4psu_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4psu_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4psu ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4psu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32181.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: ATCC BAA-98 / CGA009 / Gene: RPA1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N9M9, Hydrolases |
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#2: Chemical | ChemComp-12P / |
#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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M potassium thiocyanate, 20% PEG3350, 4% Jeffmine M-600, 1/300 trypsin, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32 Å / Num. all: 16900 / Num. obs: 16885 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.24 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→31.961 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 23.77 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→31.961 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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