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Yorodumi- PDB-2g3a: Crystal structure of putative acetyltransferase from Agrobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g3a | ||||||
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Title | Crystal structure of putative acetyltransferase from Agrobacterium tumefaciens | ||||||
Components | acetyltransferase | ||||||
Keywords | TRANSFERASE / acetyltransferase / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens str. C58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Cymborowski, M. / Xu, X. / Chruszcz, M. / Zheng, H. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative acetyltransferase from Agrobacterium tumefaciens Authors: Cymborowski, M. / Xu, X. / Chruszcz, M. / Zheng, H. / Gu, J. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g3a.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g3a.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 2g3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3a ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3a | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17203.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold (DE3) / References: UniProt: Q7CXI0 |
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#2: 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: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Hepes, pH 8.0, 0.1M CaCl2, 28% PEG 400, 3% MPD, 1mM AcetylCOA, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å |
Detector | Type: SBC / Detector: CCD / Date: Feb 10, 2006 / Details: Mirrors |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 13028 / Num. obs: 13028 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.9→1.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / Num. unique all: 337 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.53 / SU ML: 0.101 / SU R Cruickshank DPI: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.138 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.492 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.943 Å / Total num. of bins used: 20
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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