+Open data
-Basic information
Entry | Database: PDB / ID: 3ohp | ||||||
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Title | Crystal structure of HGPRT from Vibrio cholerae | ||||||
Components | Hypoxanthine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / phosphoribosyltransferase | ||||||
Function / homology | Function and homology information adenine salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding ...adenine salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Kim, J. / Ramagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of HGPRT from Vibrio cholerae Authors: Kim, J. / Ramagopal, U.A. / Almo, S.C. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ohp.cif.gz | 278.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ohp.ent.gz | 228.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ohp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ohp_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 3ohp_full_validation.pdf.gz | 469.5 KB | Display | |
Data in XML | 3ohp_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 3ohp_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/3ohp ftp://data.pdbj.org/pub/pdb/validation_reports/oh/3ohp | HTTPS FTP |
-Related structure data
Related structure data | 1g9sS 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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Unit cell |
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-Components
#1: Protein | Mass: 20135.090 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: hpt, VC_0585 / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q9KUD7, hypoxanthine phosphoribosyltransferase #2: 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: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M citrate PH 5.5, 20% PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 47025 / Num. obs: 46597 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.058 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4386 / Rsym value: 0.294 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G9S Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.576 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.167 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.038→2.091 Å / 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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