+Open data
-Basic information
Entry | Database: PDB / ID: 4i5t | ||||||
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Title | Crystal structure of yeast Ap4A phosphorylase Apa2 | ||||||
Components | 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 | ||||||
Keywords | TRANSFERASE / Ap4A phosphorylase / Ap4A | ||||||
Function / homology | Function and homology information sulfate adenylyltransferase (ADP) / sulfate adenylyltransferase (ADP) activity / ATP adenylyltransferase / bis(5'-nucleosyl)-tetraphosphatase activity / ATP:ADP adenylyltransferase activity / nucleotide biosynthetic process / nucleoside catabolic process / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Jiang, Y.L. / Hou, W.T. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structures of yeast Apa2 reveal catalytic insights into a canonical AP4A phosphorylase of the histidine triad superfamily Authors: Hou, W.T. / Li, W.Z. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i5t.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i5t.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 4i5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i5t_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 4i5t_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 4i5t_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 4i5t_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/4i5t ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i5t | HTTPS FTP |
-Related structure data
-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
#1: Protein | Mass: 37902.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: APA2, YDR530C, D9719.33 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22108, ATP adenylyltransferase #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: 2.03 Å3/Da / Density % sol: 39.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG 2K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.49 Å / Num. obs: 27391 / % possible obs: 97.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→44.844 Å / SU ML: 0.74 / σ(F): 1.35 / Phase error: 29.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.629 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.844 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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