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Yorodumi- PDB-1njr: Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njr | ||||||
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Title | Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase | ||||||
Components | 32.1 kDa protein in ADH3-RCA1 intergenic region | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dimer / Two domain organization / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information tRNA splicing, via endonucleolytic cleavage and ligation / ADP-ribose 1''-phosphate phosphatase / phosphatase activity Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Kumaran, D. / Eswaramoorthy, S. / Studier, F.W. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme Authors: Kumaran, D. / Eswaramoorthy, S. / Studier, F.W. / Swaminathan, S. | ||||||
History |
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Remark 300 | BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ...BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1njr.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1njr.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1njr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1njr_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 1njr_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 1njr_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1njr_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njr ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the crystallographic two fold axis |
-Components
#1: Protein | Mass: 32575.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YMR087W or YM9582.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04299 |
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#2: Sugar | ChemComp-XYL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.91 % Description: High resolution data for this structure was collected at X25 of NSLS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG 6000, Citric acid, Xylitol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 24, 2002 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 18988 / Num. obs: 18988 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.266 / Num. unique all: 1620 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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