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Yorodumi- PDB-3vbi: Crystal Structure of AntD, an N-acyltransferase from Bacillus cer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vbi | ||||||
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Title | Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A | ||||||
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 / dTDP-4-amino-4,6-dideoxyglucose / BICARBONATE ION / COENZYME A / : 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 | 3vbi.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vbi.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vbi_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 3vbi_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3vbi_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3vbi_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/3vbi ftp://data.pdbj.org/pub/pdb/validation_reports/vb/3vbi | HTTPS FTP |
-Related structure data
Related structure data | 3vbjC 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
-Protein , 1 types, 3 molecules ACE
#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 |
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-Non-polymers , 5 types, 308 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.56 Å3/Da / Density % sol: 51.94 % |
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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 9, 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→38.659 Å / Num. all: 63508 / Num. obs: 57751 / % possible obs: 90.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 1.6 / Num. unique all: 7460 / Rsym value: 0.249 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MIR MODEL Resolution: 1.8→38.659 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.476 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.138 / 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: 27.478 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.659 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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