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Yorodumi- PDB-3vbn: Crystal Structure of the D94A mutant of AntD, an N-acyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vbn | ||||||
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Title | Crystal Structure of the D94A mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP and Coenzyme A | ||||||
Components | Galactoside O-acetyltransferaseGalactoside acetyltransferase | ||||||
Keywords | TRANSFERASE / anthrose / acylated sugar / left-handed beta helix / sugar N-acylation | ||||||
Function / homology | Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Mainly Beta / COENZYME A / THYMIDINE-5'-DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kubiak, R.L. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural Studies of AntD: An N-Acyltransferase Involved in the Biosynthesis of d-Anthrose. Authors: Kubiak, R.L. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vbn.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vbn.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/3vbn ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vbn | HTTPS FTP |
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-Related structure data
Related structure data | 3vbiC 3vbjC 3vbkC 3vblC 3vbmC 3vbpC C: citing same article (ref.) |
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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: 22708.283 Da / Num. of mol.: 3 / Mutation: D94A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: SJ1 / Gene: antd, BCSJ1_02085 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 References: UniProt: D7WGJ0, galactoside O-acetyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #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: 2.55 Å3/Da / Density % sol: 51.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% pentaerythritol ethoxylate (3/4 EO/OH), 2% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 29, 2011 / Details: Montel |
Radiation | Monochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.599 Å / Num. all: 23813 / Num. obs: 22486 / % possible obs: 94.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2201 / Rsym value: 0.38 / % possible all: 80.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MIR MODEL Resolution: 2.5→40.599 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.869 / SU B: 11.588 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.836 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40.599 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.561 Å / Total num. of bins used: 20
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