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Yorodumi- PDB-2wlf: Crystallographic analysis of the polysialic acid O-acetyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wlf | ||||||
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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 / cytosol Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wlf.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wlf.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wlf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2wlf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2wlf_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2wlf_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlf ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 6 - 214 / Label seq-ID: 6 - 214
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-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: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ...ENGINEERED | |
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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: 2.65 Å3/Da / Density % sol: 54 % Description: STARTING MODEL WAS MY NAI SOAKING SIRAS STRUCTURE SOLVED BY SHELX-CDE. |
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Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE, 2.25 M AMMONIUM ACETATE, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 |
Detector | Type: MBC NOIR-1 / Detector: CCD / Date: Jun 26, 2008 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 32150 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE STRUCTURE Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.141 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 12.783 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→40 Å
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Refine LS restraints |
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