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Yorodumi- PDB-1yvw: Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yvw | ||||||
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Title | Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13. | ||||||
Components | Phosphoribosyl-ATP pyrophosphatase | ||||||
Keywords | HYDROLASE / HELIX BUNDLE / HISTIDINE BIOSYNTHESIS / pyrophosphatase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Benach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Shastry, R. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus at 2.6 A resolution. Authors: Benach, J. / Kuzin, A.P. / Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Shastry, R. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yvw.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvw.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvw ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the a.u. contains the putative biological assembly |
-Components
#1: Protein | Mass: 13678.231 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: hisE / Production host: Escherichia coli (E. coli) References: UniProt: Q81G00, phosphoribosyl-ATP diphosphatase #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 Å3/Da / Density % sol: 38.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 3.5 M NaFormate, 50mM NaAcetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927 / Wavelength: 0.97927 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 14016 / Num. obs: 14016 / % possible obs: 80 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.32 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→29.06 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2783848.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4166 Å2 / ksol: 0.327497 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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