[English] 日本語
Yorodumi- PDB-2wld: Crystallographic analysis of the polysialic acid O-acetyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wld | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic analysis of the polysialic acid O-acetyltransferase OatWY | ||||||
Components | POLYSIALIC ACID O-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ENZYME / ACETYLTRANSFERASE / LEFT-HANDED BETA HELIX | ||||||
Function / homology | Function and homology information polysialic-acid O-acetyltransferase activity / protein homotrimerization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase Oatwy from Neisseria Meningitidis. Authors: Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wld.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wld.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wld ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wld | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 23731.191 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LEFT-HANDED BETA HELIX Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria) Strain: 406Y / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: Q93S40 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % Description: STARTING MODEL WAS MY NAI SOAKING SIRAS STRUCTURE SOLVED BY SHELX-CDE. |
---|---|
Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE, PH 4.6, 2.25 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 39235 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 8.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE STRUCTURE Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.32 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.881 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|