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Yorodumi- PDB-2yvp: Crystal structure of NDX2 in complex with MG2+ and ampcpr from th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yvp | ||||||
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Title | Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8 | ||||||
Components | MutT/nudix family protein | ||||||
Keywords | HYDROLASE / NUDIX PROTEIN / ADP-RIBOSE / FAD / THERMUS THERMOPHILUS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Wakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2008 Title: Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8 Authors: Wakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yvp.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yvp.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yvp_validation.pdf.gz | 917.3 KB | Display | wwPDB validaton report |
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Full document | 2yvp_full_validation.pdf.gz | 921.6 KB | Display | |
Data in XML | 2yvp_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2yvp_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvp ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvp | HTTPS FTP |
-Related structure data
Related structure data | 2yvmSC 2yvnC 2yvoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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
#1: Protein | Mass: 20336.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ndx2 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SJY9, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | #3: Chemical | ChemComp-RBY / | #4: 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: 2.45 Å3/Da / Density % sol: 49.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.033M MES, 0.053M MAGNESIUM ACETATE, 4.7%(W/V) PEG8000, 6.7%(W/V) GLYCEROL, 10mM AMPCPR, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 5, 2005 |
Radiation | Monochromator: TRANSPARENT DIAMOND DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. all: 23576 / Num. obs: 23576 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 51.3 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 14 / Num. unique all: 2284 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YVM Resolution: 1.66→24.34 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.66→24.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.76 Å / Rfactor Rfree error: 0.011
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