+Open data
-Basic information
Entry | Database: PDB / ID: 6asv | ||||||
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Title | E. coli PRPP Synthetase | ||||||
Components | Ribose-phosphate pyrophosphokinase | ||||||
Keywords | TRANSFERASE / nucleotide biosynthesis phosphoribosyl pyrophosphate KPRS | ||||||
Function / homology | Function and homology information ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å | ||||||
Authors | French, J.B. / Zhou, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: BMC Struct. Biol. / Year: 2019 Title: Crystal structure of E. coli PRPP synthetase. Authors: Zhou, W. / Tsai, A. / Dattmore, D.A. / Stives, D.P. / Chitrakar, I. / D'alessandro, A.M. / Patil, S. / Hicks, K.A. / French, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6asv.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6asv.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 6asv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/6asv ftp://data.pdbj.org/pub/pdb/validation_reports/as/6asv | HTTPS FTP |
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-Related structure data
Related structure data | 3dahS 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: 36426.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: prs, prsA, Z1978, ECs1712 / Production host: Escherichia coli (E. coli) References: UniProt: P0A719, ribose-phosphate diphosphokinase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium Chloride 0.1 M Hepes, pH 7.5 30% w/v PEG 400 1 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.21→50 Å / Num. obs: 49727 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Χ2: 0.787 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 3DAH Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.339 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.187 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 135.04 Å2 / Biso mean: 52.152 Å2 / Biso min: 31.08 Å2
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Refinement step | Cycle: final / Resolution: 2.21→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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