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Yorodumi- PDB-3s6m: The structure of a Peptidyl-prolyl cis-trans isomerase from Burkh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s6m | ||||||
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Title | The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei | ||||||
Components | Peptidyl-prolyl cis-trans isomerase | ||||||
Keywords | ISOMERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Peptidyl-prolyl cis-trans isomerase | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.651 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei Authors: Clifton, M.C. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s6m.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s6m.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3s6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s6m_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 3s6m_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 3s6m_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 3s6m_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6m ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6m | HTTPS FTP |
-Related structure data
Related structure data | 2nulS 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: 18211.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_2684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JQT3, peptidylprolyl isomerase | ||
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#2: Chemical | ChemComp-EDO / | ||
#3: Chemical | #4: 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: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 50% PEG 400, 0.1M NaAcetate pH 4.5, 200mM Lithium sulfate. Direct cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 23, 2011 / Details: VariMax Cu-HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 19225 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.112 / Χ2: 2.365 / Net I/σ(I): 23.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 46.35 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NUL Resolution: 1.651→23.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2021 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9053 / SU B: 2.851 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0839 / SU Rfree: 0.0865 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.91 Å2 / Biso mean: 16.5407 Å2 / Biso min: 5.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.651→23.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 6.3107 Å / Origin y: 29.0866 Å / Origin z: 5.3101 Å
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