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Yorodumi- PDB-3f0a: Structure of a putative n-acetyltransferase (ta0374) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0a | ||||||
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Title | Structure of a putative n-acetyltransferase (ta0374) in complex with acetyl-coa from thermoplasma acidophilum | ||||||
Components | N-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / N-ACETYLTRANSFERASE / THERMOPLASMA ACIDOPHILUM / ACETYL-COA / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information negative regulation of sporulation / diamine N-acetyltransferase / diamine N-acetyltransferase activity Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production. Authors: Filippova, E.V. / Shuvalova, L. / Minasov, G. / Kiryukhina, O. / Zhang, Y. / Clancy, S. / Radhakrishnan, I. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f0a.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f0a.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f0a_validation.pdf.gz | 714.9 KB | Display | wwPDB validaton report |
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Full document | 3f0a_full_validation.pdf.gz | 716 KB | Display | |
Data in XML | 3f0a_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3f0a_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0a ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0a | HTTPS FTP |
-Related structure data
Related structure data | 3fixC 3k9uC 3ne7C 1tiqS 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: 19221.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0374 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q9HL57 |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACO / |
#5: 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: 2.83 Å3/Da / Density % sol: 56.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M Na Acetate, 30% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 |
Detector | Detector: CCD / Date: Oct 10, 2008 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→54.55 Å / Num. obs: 7926 / % possible obs: 20.8 % / Observed criterion σ(I): -3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.49 / Rsym value: 0.49 / Net I/σ(I): 3.794 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1 % / Mean I/σ(I) obs: 0.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 1TIQ Resolution: 2.5→54.55 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.391 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→54.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.8578 Å / Origin y: 5.9877 Å / Origin z: -16.4347 Å
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