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Yorodumi- PDB-4dmo: Crystal structure of the (BACCR)NAT3 arylamine N-acetyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dmo | ||||||
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Title | Crystal structure of the (BACCR)NAT3 arylamine N-acetyltransferase from Bacillus cereus reveals a unique Cys-His-Glu catalytic triad | ||||||
Components | N-hydroxyarylamine O-acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetyltransferase | ||||||
Function / homology | Function and homology information N-hydroxyarylamine O-acetyltransferase / N-hydroxyarylamine O-acetyltransferase activity / arylamine N-acetyltransferase activity Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Kubiak, X. / Li de la Sierra-Gallay, I. / Haouz, A. / Weber, P. / Rodrigues-Lima, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Biochemical Characterization of an Active Arylamine N-Acetyltransferase Possessing a Non-canonical Cys-His-Glu Catalytic Triad. Authors: Kubiak, X. / Li de la Sierra-Gallay, I. / Chaffotte, A.F. / Pluvinage, B. / Weber, P. / Haouz, A. / Dupret, J.M. / Rodrigues-Lima, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dmo.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dmo.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dmo_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 4dmo_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 4dmo_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 4dmo_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/4dmo ftp://data.pdbj.org/pub/pdb/validation_reports/dm/4dmo | HTTPS FTP |
-Related structure data
Related structure data | 3lnbS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30100.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Cellular location: Cytosol / Gene: BC_3483, NAT3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q81AS3, N-hydroxyarylamine O-acetyltransferase #2: Chemical | #3: 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: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.37 M sodium citrate, 0.28 M NDSB-221, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.984 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2011 / Details: collimating (M1) and toroidal (M2) mirrors |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→19.967 Å / Num. obs: 28380 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.392 % / Biso Wilson estimate: 45.83 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 19.07 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 7.25 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.28 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LNB Resolution: 2.14→19.95 Å / Cor.coef. Fo:Fc: 0.9417 / Cor.coef. Fo:Fc free: 0.9062 / SU ML: 0.28 / SU R Cruickshank DPI: 0.593 / σ(F): 1.99 / Phase error: 31.95 / Stereochemistry target values: ML Details: Additional restraint dictionnary file used through the Gelly module implemented in Buster: protgeo_option_chiralrestraint_from_equilib.dat
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.341 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→19.95 Å
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Refine LS restraints |
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LS refinement shell |
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