+Open data
-Basic information
Entry | Database: PDB / ID: 2dy0 | ||||||
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Title | Crystal structure of project JW0458 from Escherichia coli | ||||||
Components | Adenine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / magnesium ion binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of JW0458 from Escherichia coli Authors: Shimizu, K. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dy0.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dy0.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dy0_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 2dy0_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 2dy0_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2dy0_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dy0 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dy0 | HTTPS FTP |
-Related structure data
Related structure data | 1zn9S 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: 20400.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K12, W3110 / Description: cell free / Plasmid: px060316-06 References: UniProt: P69503, adenine phosphoribosyltransferase #2: Chemical | ChemComp-MG / | #3: 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: 2.13 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 291 K / Method: microbach / pH: 8.5 Details: 30 w/v(%) PEG 4000, 0.1M Tris, 0.2M Mg Chlor , pH 8.5, Microbach, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 6, 2006 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→40 Å / Num. all: 88230 / Num. obs: 88230 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.052 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.207 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1ZN9 Resolution: 1.25→35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 707686.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.533 Å2 / ksol: 0.342346 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.25→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.33 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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