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Yorodumi- PDB-1mqe: Structure of the MT-ADPRase in complex with gadolidium and ADP-ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqe | ||||||
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Title | Structure of the MT-ADPRase in complex with gadolidium and ADP-ribose, a Nudix enzyme | ||||||
Components | ADPR pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix hydrolase / Rv1700 / ADPR / Mycobacterium Tuberculosis | ||||||
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 / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Kang, L.-W. / Gabelli, S.B. / Bianchet, M.A. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure and mechanism of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis Authors: Kang, L.-W. / Gabelli, S.B. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqe.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqe.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mqe_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 1mqe_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1mqe_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1mqe_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqe ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 22920.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): blr(de3) / References: UniProt: O33199, ADP-ribose diphosphatase |
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#2: Chemical | ChemComp-APR / |
#3: Chemical | ChemComp-GD3 / |
#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: 2.35 Å3/Da / Density % sol: 47.72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium formate, Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 15835 / Num. obs: 15604 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.075 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.336 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 127268 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 97.5 % / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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