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Yorodumi- PDB-3efe: The crystal structure of the thiJ/pfpI family protein from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3efe | ||||||
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Title | The crystal structure of the thiJ/pfpI family protein from Bacillus anthracis | ||||||
Components | ThiJ/pfpI family protein | ||||||
Keywords | CHAPERONE / thiJ/pfpI family protein / Bacillus anthracis / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
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 / Glutamine amidotransferase / ThiJ/pfpI family protein Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the thiJ/pfpI family protein from Bacillus anthracis Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3efe.cif.gz | 250.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3efe.ent.gz | 204.3 KB | Display | PDB format |
PDBx/mmJSON format | 3efe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3efe_validation.pdf.gz | 493.9 KB | Display | wwPDB validaton report |
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Full document | 3efe_full_validation.pdf.gz | 546.9 KB | Display | |
Data in XML | 3efe_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 3efe_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efe ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efe | 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: 23783.445 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2475, BA_2657, GBAA2657 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81PY3, UniProt: A0A6H3AJL8*PLUS #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Sequence details | THE TARGET ID IDP01712 DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING | |
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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: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Heoes, 0.2M NH4(OAC0), 25% PEG3350, pH 7.5, 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-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→83.62 Å / Num. all: 55865 / Num. obs: 54826 / % possible obs: 98.14 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.3→2.359 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.65 / Num. unique all: 4303 / % possible all: 83.29 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→83.62 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.854 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.374 / ESU R Free: 0.239 / 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: 38.249 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→83.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 83.497 Å / Origin y: 3.89 Å / Origin z: 25.68 Å
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Refinement TLS group |
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