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Yorodumi- PDB-6kqc: Crystal structure of E136F mutant of Xanthine-guanine phosphoribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kqc | ||||||
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Title | Crystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis | ||||||
Components | Xanthine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / E136F mutant / xanthine-guanine phosphoribosyltransferase / Yersinia pestis | ||||||
Function / homology | Function and homology information xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lankipalli, S. / Ramagopal, U.A. | ||||||
Citation | Journal: To be published Title: Crystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis Authors: Lankipalli, S. / 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 | 6kqc.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kqc.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kqc ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kqc | HTTPS FTP |
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-Related structure data
Related structure data | 5xtkS 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: 17090.654 Da / Num. of mol.: 2 / Mutation: E136F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: gpt, YPO3225, y0963, YP_0708 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8ZC05, xanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.03 Å3/Da / Density % sol: 39.52 % / Mosaicity: 1.2 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Lithium chloride, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→37.86 Å / Num. obs: 30317 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XTK Resolution: 1.7→37.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.361 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 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: 54.22 Å2 / Biso mean: 15.591 Å2 / Biso min: 9.16 Å2
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Refinement step | Cycle: final / Resolution: 1.7→37.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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