+Open data
-Basic information
Entry | Database: PDB / ID: 2c84 | ||||||
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Title | CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE PM0188 WITH CMP | ||||||
Components | ALPHA-2,3/2,6-SIALYLTRANSFERASE/SIALIDASE | ||||||
Keywords | TRANSFERASE / HYPOTHETICAL PROTEIN / PM0188 / SIALYLTRANSFERASE / CMP / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Kim, D.U. / Cho, H.S. | ||||||
Citation | Journal: Bmb Rep / Year: 2008 Title: Structural analysis of sialyltransferase PM0188 from Pasteurella multocida complexed with donor analogue and acceptor sugar. Authors: Kim, D.U. / Yoo, J.H. / Lee, Y.J. / Kim, K.S. / Cho, H.S. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural Analysis of the Sialyltransferase Cstii from Campylobacter Jejuni in Complex with a Substrate Analog Authors: Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c84.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c84.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c84 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c84 | HTTPS FTP |
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-Related 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: 45534.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pasteurella multocida / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15KI8 |
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#2: Chemical | ChemComp-C / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.22 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 26832 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.99 / % possible all: 80.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→55.56 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.873 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / 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: 23.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→55.56 Å
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