[English] 日本語
Yorodumi- PDB-3q3i: Crystal structure of the Actinobacillus pleuropneumoniae HMW1C gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q3i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Actinobacillus pleuropneumoniae HMW1C glycosyltransferase in the presence of peptide N1131 | ||||||
Components | HMW1C-like glycosyltransferase | ||||||
Keywords | TRANSFERASE / HMW1C / HMW1 / N-glycosylation | ||||||
Function / homology | Rossmann fold - #11380 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Actinobacillus pleuropneumoniae serovar 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.45 Å | ||||||
Authors | Kawai, F. / Yeo, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Insights into the Glycosyltransferase Activity of the Actinobacillus pleuropneumoniae HMW1C-like Protein. Authors: Kawai, F. / Grass, S. / Kim, Y. / Choi, K.J. / St Geme, J.W. / Yeo, H.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q3i.cif.gz | 248.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q3i.ent.gz | 199.9 KB | Display | PDB format |
PDBx/mmJSON format | 3q3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q3i_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3q3i_full_validation.pdf.gz | 490.3 KB | Display | |
Data in XML | 3q3i_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 3q3i_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/3q3i ftp://data.pdbj.org/pub/pdb/validation_reports/q3/3q3i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 71870.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus pleuropneumoniae serovar 1 (bacteria) Strain: 4074 / Gene: APL_1635, appser1_17560 / Plasmid: PET45B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0EAD4 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Sequence details | S428P POSSIBLE NATURAL VARIANT | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 0.1-0.16 M ammonium sulfate, 20-30% w/v PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2009 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 46099 / % possible obs: 94.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.303 / % possible all: 83.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR / Resolution: 2.45→49.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 9.132 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.56 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→49.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.52 Å / Total num. of bins used: 20
|