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Yorodumi- PDB-3vbj: Crystal Structure of AntD, an N-acyltransferase from Bacillus cer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vbj | ||||||
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Title | Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP and 3-hydroxybutyryl-CoA | ||||||
Components | Galactoside O-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 / 3-HYDROXYBUTANOYL-COENZYME A / THYMIDINE-5'-DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3vbj.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vbj.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vbj_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 3vbj_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3vbj_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3vbj_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/3vbj ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vbj | HTTPS FTP |
-Related structure data
Related structure data | 3vbiC 3vbkC 3vblC 3vbmC 3vbnC 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: 22752.293 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: SJ1 / Gene: antd, BCSJ1_02085 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 References: UniProt: D7WGJ0, galactoside O-acetyltransferase #2: Chemical | ChemComp-CL / | #3: Chemical | #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: 2.55 Å3/Da / Density % sol: 51.85 % |
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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: May 11, 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: 1.8→31.72 Å / Num. all: 63474 / Num. obs: 60265 / % possible obs: 94.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7806 / Rsym value: 0.29 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MIR MODEL Resolution: 1.8→31.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.852 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY STRUCTURE FACTOR FILE CONTAINS NO FREE R TEST SET FLAGS.
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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: 25.666 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20
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