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Yorodumi- PDB-3fk8: The crystal structure of disulphide isomerase from Xylella fastid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fk8 | ||||||
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Title | The crystal structure of disulphide isomerase from Xylella fastidiosa Temecula1 | ||||||
Components | Disulphide isomerase | ||||||
Keywords | ISOMERASE / APC61824.1 / disulphide isomerase / Xylella fastidiosa Temecula1 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xylella fastidiosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Tan, K. / Sather, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of disulphide isomerase from Xylella fastidiosa Temecula1 Authors: Tan, K. / Sather, A. / Shackelford, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fk8.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fk8.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fk8 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fk8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | authors state that biological unit is experimentally unknown, and is predicted to be monomeric. |
-Components
#1: Protein | Mass: 14777.548 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Temecula1 / Gene: PD_1033, Xylella fastidiosa / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87CN2 | ||
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#2: Chemical | ChemComp-FMT / #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: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 0.2M Trimethylamine N-oxide, 20% PEG MME 2000, pH 8.5, 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-ID / Wavelength: 0.97942 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→27.54 Å / Num. all: 29212 / Num. obs: 29212 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.76 / Num. unique all: 1426 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→27.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.555 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.051 / 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: 18.859 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→27.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.302→1.336 Å / Total num. of bins used: 20
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