[English] 日本語
Yorodumi- PDB-1spv: Crystal Structure of the Putative Phosphatase of Escherichia coli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1spv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Putative Phosphatase of Escherichia coli, Northeast Structural Genomoics Target ER58 | ||||||
Components | putative polyprotein/phosphatase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomoics / alpha/beta monomeric protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information O-acetyl-ADP-ribose deacetylase / regulation of single-species biofilm formation on inanimate substrate / purine nucleoside metabolic process / purine nucleoside binding / O-acetyl-ADP-ribose deacetylase activity / endoribonuclease inhibitor activity / response to antibiotic / enzyme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Phosphatase of Escherichia coli, Northeast Structural Genomoics Target ER58 Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1spv.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1spv.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 1spv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1spv_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1spv_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 1spv_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1spv_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/1spv ftp://data.pdbj.org/pub/pdb/validation_reports/sp/1spv | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19904.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P0A8D6 |
---|---|
#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.13 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Well solution: 12% PEG 20K, 100mM MES pH 5.75, 30mM KH2PO4. Protein Solution: 10mM Tris pH 7.5, 5mM DTT, 100mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.29 Å / Num. obs: 22088 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.15 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.065 / Net I/σ(I): 18.84 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.7 / Num. unique all: 2214 / Rsym value: 0.116 / % possible all: 97.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2→29.29 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.29 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018
|