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Yorodumi- PDB-4nv8: Crystal Structure of Mesorhizobium Loti Arylamine N-acetyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nv8 | ||||||
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Title | Crystal Structure of Mesorhizobium Loti Arylamine N-acetyltransferase F42W Mutant | ||||||
Components | Arylamine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / NAT / Arylamine N-acetyltransferase / acetyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mesorhizobium loti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Xu, X.M. / Haouz, A. / Weber, P. / Li de la sierra-gallay, I. / Kubiak, X. / Dupret, J.-M. / Rodrigues-lima, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Insight into cofactor recognition in arylamine N-acetyltransferase enzymes: structure of Mesorhizobium loti arylamine N-acetyltransferase in complex with coenzyme A. Authors: Xu, X. / Li de la Sierra-Gallay, I. / Kubiak, X. / Duval, R. / Chaffotte, A.F. / Dupret, J.M. / Haouz, A. / 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 | 4nv8.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nv8.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nv8_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 4nv8_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 4nv8_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4nv8_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/4nv8 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/4nv8 | HTTPS FTP |
-Related structure data
Related structure data | 4nv7C 2bszS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 5 - 275 / Label seq-ID: 39 - 309
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-Components
#1: Protein | Mass: 34361.777 Da / Num. of mol.: 2 / Mutation: F42W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr4870 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q98D42, arylamine N-acetyltransferase #2: 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: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 5000, 0.2M ammonium sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07169 Å |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07169 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→32.01 Å / Num. obs: 61856 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.064 / Rsym value: 0.071 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.682 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BSZ Resolution: 1.84→32.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.886 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.561 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→32.01 Å
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Refine LS restraints |
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