[English] 日本語
Yorodumi- PDB-9b22: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b22 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose and AMP bound) | |||||||||
Components | ADP-ribose pyrophosphatase | |||||||||
Keywords | HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase | |||||||||
Function / homology | Function and homology information ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To be published Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose and AMP bound) Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9b22.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9b22.ent.gz | 159.4 KB | Display | PDB format |
PDBx/mmJSON format | 9b22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b22_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9b22_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 9b22_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 9b22_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/9b22 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/9b22 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24742.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45750 / Plasmid: KlpnC.20447.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GVQ7, ADP-ribose diphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-AMP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D- ...Details: 23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D-ribose form. Subunit B contains AMP and ADP-ribose in the active site and were refined with grouped occupancies. plate Liu-S-102, F8. Puck: PSL-1011, Cryo: 10% extra PEG 4000 added to the drop. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 10, 2024 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→36.58 Å / Num. obs: 100227 / % possible obs: 97.7 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 0.95 / Net I/σ(I): 14.3 / Num. measured all: 641274 |
Reflection shell | Resolution: 1.3→1.33 Å / % possible obs: 80 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.692 / Num. measured all: 25108 / Num. unique obs: 6043 / CC1/2: 0.695 / Rpim(I) all: 0.377 / Rrim(I) all: 0.793 / Χ2: 0.9 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→36.58 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.92 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→36.58 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|