[English] 日本語
Yorodumi- PDB-3occ: Crystal structure of PNP with DADMEimmH from Yersinia pseudotuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3occ | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis | |||||||||
Components | Purine nucleoside phosphorylase deoD-type | |||||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | |||||||||
Function / homology | Function and homology information purine nucleoside metabolic process / nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Yersinia pseudotuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Kim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | |||||||||
Citation | Journal: To be Published Title: crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis Authors: Kim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3occ.cif.gz | 551.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3occ.ent.gz | 455.5 KB | Display | PDB format |
PDBx/mmJSON format | 3occ.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3occ_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3occ_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3occ_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 3occ_validation.cif.gz | 93.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3occ ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3occ | HTTPS FTP |
-Related structure data
Related structure data | 1pr0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25965.881 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: YPIII / Gene: deoD, YPK_3624 / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: B1JL34, purine-nucleoside phosphorylase #2: Chemical | ChemComp-DIH / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 150mM DL-malic acid, 20% PEG3350, pH 7.0, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 171125 / Num. obs: 171125 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.069 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.48 / Num. unique all: 16923 / Rsym value: 0.549 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PR0 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.563 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.613 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|