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Yorodumi- PDB-4rqb: Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rqb | ||||||
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Title | Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group) | ||||||
Components | Hypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / PRTase / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / : Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Ghosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686) from Staphylococcus aureus (tetragonal space group) Authors: Ghosh, A. / Ahmed, A. / Bhoshle, R. / Seidel, R. / Stead, M. / Toro, R. / Schramm, V.L. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rqb.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rqb.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/4rqb ftp://data.pdbj.org/pub/pdb/validation_reports/rq/4rqb | HTTPS FTP |
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-Related structure data
Related structure data | 4rqaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21239.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: USA300_TCH1516 / Gene: hpt / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRIL References: UniProt: A8YZK8, hypoxanthine phosphoribosyltransferase |
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-Non-polymers , 5 types, 77 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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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: 3.54 Å3/Da / Density % sol: 65.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium Cacodylate, 1.26 M Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 6, 2013 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. all: 43010 / Num. obs: 42955 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4RQA Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.369 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Unmodeled densities present near Thr112 of both protomers (chain A and B)
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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: 30.947 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→30 Å
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Refine LS restraints |
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