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Yorodumi- PDB-3x0m: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x0m | ||||||
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Title | ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-state at reaction time of 3 min | ||||||
Components | ADP-ribose pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix motif / ADP ribose hydrolase / ADP ribose / Cytosol | ||||||
Function / homology | Function and homology information guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / UDP-sugar diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors Authors: Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x0m.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x0m.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x0m_validation.pdf.gz | 789.2 KB | Display | wwPDB validaton report |
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Full document | 3x0m_full_validation.pdf.gz | 792.6 KB | Display | |
Data in XML | 3x0m_validation.xml.gz | 11 KB | Display | |
Data in CIF | 3x0m_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/3x0m ftp://data.pdbj.org/pub/pdb/validation_reports/x0/3x0m | HTTPS FTP |
-Related structure data
Related structure data | 3x0iSC 3x0jC 3x0kC 3x0lC 3x0nC 3x0oC 3x0pC 3x0qC 3x0rC 3x0sC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19287.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA0528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW5, ADP-ribose diphosphatase |
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-Non-polymers , 5 types, 148 molecules
#2: Chemical | ChemComp-AR6 / [( |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-MN / |
#6: 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: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ES100=0.24M Acetate-Sodium acetate buffer, 0.32M Ammonium sulfate, 30%(w/v) Glycerol, 9%(w/v) PEG 20000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.15→20 Å / Num. all: 60829 / Num. obs: 60829 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X0I Resolution: 1.15→20 Å / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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Refine LS restraints |
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