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Yorodumi- PDB-3wo5: Crystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wo5 | ||||||
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Title | Crystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis | ||||||
Components | AP-4-A phosphorylase | ||||||
Keywords | TRANSFERASE / Mycobacterium / diadenosine polyphosphate / phosphorylase / HIT motif | ||||||
Function / homology | Function and homology information diadenosine tetraphosphate catabolic process / ATP adenylyltransferase / bis(5'-nucleosyl)-tetraphosphatase activity / ATP:ADP adenylyltransferase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Mori, S. / Wachino, J. / Arakawa, Y. / Shibayama, K. | ||||||
Citation | Journal: To be Published Title: Role of Ser-147 and Ala-149 in catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv Authors: Mori, S. / Wachino, J. / Kim, H. / Rimbara, E. / Arakawa, Y. / Shibayama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wo5.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wo5.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3wo5 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3wo5 | HTTPS FTP |
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-Related structure data
Related structure data | 3anoS S: Starting model for refinement |
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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
#1: Protein | Mass: 24784.037 Da / Num. of mol.: 2 / Mutation: S147Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2688, Rv2613c / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: O06201, UniProt: P9WMK9*PLUS, ATP adenylyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1M sodium cacodylate, 0.2M lithium sulfate, 28.5% polyethylene glycol 400, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. all: 11717 / Num. obs: 11269 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.79→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Num. unique all: 518 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ANO Resolution: 2.79→31.775 Å / FOM work R set: 0.8834 / SU ML: 0.38 / σ(F): 0.8 / Phase error: 19.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.533 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.16 Å2 / Biso mean: 20.95 Å2 / Biso min: 7.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→31.775 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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