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- PDB-9b1z: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9b1z | |||||||||
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Title | Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (Apo) | |||||||||
![]() | ADP-ribose pyrophosphatase | |||||||||
![]() | HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (Apo) Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.6 KB | Display | ![]() |
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PDB format | ![]() | 159.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.5 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24742.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 33% Peg 3350, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-102, C1. Puck: PSL-1001, Cryo: direct. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.25→45.58 Å / Num. obs: 99570 / % possible obs: 93.3 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Χ2: 0.91 / Net I/σ(I): 15 / Num. measured all: 609044 |
Reflection shell | Resolution: 1.25→1.28 Å / % possible obs: 55 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.441 / Num. measured all: 11802 / Num. unique obs: 4291 / CC1/2: 0.717 / Rpim(I) all: 0.302 / Rrim(I) all: 0.539 / Χ2: 0.95 / Net I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→45.58 Å
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Refine LS restraints |
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LS refinement shell |
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