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Yorodumi- PDB-4hcj: Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcj | ||||||
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Title | Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii | ||||||
Components | ThiJ/PfpI domain protein | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich | ||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / ThiJ/PfpI domain protein Function and homology information | ||||||
Biological species | Brachyspira murdochii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.12 Å | ||||||
Authors | Kim, Y. / Bigelow, L. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii Authors: Kim, Y. / Bigelow, L. / Jedrzejczak, R. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hcj.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hcj.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcj ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcj | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19098.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brachyspira murdochii (bacteria) / Strain: DSM 12563 / Gene: Bmur_0257 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D5U596 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-FMT / | #5: 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: 2.12 Å3/Da / Density % sol: 41.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium Chloride, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350, 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: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→50 Å / Num. all: 56517 / Num. obs: 56517 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 7.34 Å2 / Rsym value: 0.092 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 1598 / Rsym value: 0.231 / % possible all: 51.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.12→22.277 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 10.65 / Stereochemistry target values: ML Details: NUMBER OF REFLECTIONS ARE APPROXIMATELY TWO TIMES OF THAT OF OBSERVED BECAUSE I+ AND I- WERE USED IN THE FINAL ROUNDS OF REFINEMENT TO MODEL SE ATOMS BETTER (ANOMALOUS SCATTERING).
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→22.277 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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