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Yorodumi- PDB-3dr8: Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dr8 | ||||||
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Title | Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA | ||||||
Components | yncA | ||||||
Keywords | TRANSFERASE / Salmonella essential gene IDP0086 acetyltransferase cofactor acetyl-CoA / TRANSFERASE. FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES OF NIH CONTRACT NUMBER HHSN272200700058C / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Singer, A.U. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA Authors: Singer, A.U. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dr8.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dr8.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dr8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3dr8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3dr8_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 3dr8_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3dr8 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dr8 | HTTPS FTP |
-Related structure data
Related structure data | 2bl1S 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: 19673.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SNA at N-terminus following cleavage of His-tag with TEV protease Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yncA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) References: UniProt: Q8ZPD3*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-CL / #4: Chemical | #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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 295 K / pH: 5.6 Details: 1.4 M Sodium Acetate trihydrate 5.6 pH plus 5 mM Acetyl Coenzyme A, cryoprotected with N-paratone oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2008 / Details: Osmic mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 28962 / Num. obs: 28378 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.3 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: molecule A of 2BL1 Resolution: 1.95→47.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.279 / SU ML: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→47.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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