+Open data
-Basic information
Entry | Database: PDB / ID: 1mk1 | ||||||
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Title | Structure of the MT-ADPRase in complex with ADPR, a Nudix enzyme | ||||||
Components | ADPR pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix hydrolase / ADPR pyrophosphatase / ADPRase / Adenosine diphospho-ribose / Mycobacterium Tuberculosis / Rv1700 | ||||||
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 | 1mk1.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mk1.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mk1_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 1mk1_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 1mk1_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1mk1_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mk1 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mk1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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) / Gene: Rv1700 / 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: 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: 2.36 Å3/Da / Density % sol: 47.83 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium formate, Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 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: Dec 19, 2001 |
Radiation | 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. obs: 14597 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 5.86 / Rsym value: 0.281 / % possible all: 94.8 |
Reflection | *PLUS % possible obs: 92.4 % / Num. measured all: 97257 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 91.3 % / Mean I/σ(I) obs: 5.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / 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 Rfactor Rfree: 0.259 / Rfactor Rwork: 0.209 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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