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Yorodumi- PDB-5b6h: Crystal structure of an APRT from Yersinia pseudotuberculosis in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b6h | ||||||
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Title | Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP. | ||||||
Components | Adenine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / adenine phosphoribosyltransferase | ||||||
Function / homology | Function and homology information adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pseudotuberculosis serotype I | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Model details | STRUCTURAL GENOMICS | ||||||
Authors | Pavithra, G.C. / Ramagopal, U.A. | ||||||
Citation | Journal: To be published Title: Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP. Authors: Pavithra, G.C. / Ramagopal, U.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b6h.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b6h.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 5b6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b6h_validation.pdf.gz | 776.2 KB | Display | wwPDB validaton report |
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Full document | 5b6h_full_validation.pdf.gz | 776.1 KB | Display | |
Data in XML | 5b6h_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5b6h_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b6h ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b6h | HTTPS FTP |
-Related structure data
Related structure data | 4mb6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19589.320 Da / Num. of mol.: 1 / Fragment: UNP residues 7-187 Source method: isolated from a genetically manipulated source Details: AMP complex Source: (gene. exp.) Yersinia pseudotuberculosis serotype I (strain IP32953) (bacteria) Strain: IP32953 / Gene: apt, YPTB0991 / Plasmid: LIC-PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q66DQ2, adenine phosphoribosyltransferase | ||||
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#2: Chemical | ChemComp-AMP / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #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: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M sodium malonate pH 7.0 these crystals were moved condition containing 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate and soaked with 5mM AMP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→48.2 Å / Num. obs: 17719 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.054 / Net I/av σ(I): 27.149 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MB6 Resolution: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.718 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.43 Å2 / Biso mean: 26.827 Å2 / Biso min: 12.53 Å2
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Refinement step | Cycle: final / Resolution: 1.9→48.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.7073 Å / Origin y: -0.734 Å / Origin z: 7.1657 Å
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