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Yorodumi- PDB-2ex0: Crystal structure of multifunctional sialyltransferase from Paste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ex0 | ||||||
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Title | Crystal structure of multifunctional sialyltransferase from Pasteurella Multocida | ||||||
Components | a2,3-sialyltransferase, a2,6-sialyltransferase | ||||||
Keywords | TRANSFERASE / two Rossman fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ni, L. / Sun, M. / Chen, X. / Fisher, A.J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Cytidine 5'-Monophosphate (CMP)-Induced Structural Changes in a Multifunctional Sialyltransferase from Pasteurella multocida Authors: Ni, L. / Sun, M. / Yu, H. / Chokhawala, H. / Chen, X. / Fisher, A.J. | ||||||
History |
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Remark 999 | SEQUENCE Currently there is no aminoacid sequence database reference available for this protein |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ex0.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ex0.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ex0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2ex0 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2ex0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46467.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The protein has four enzymatic activities / Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: Pm70 / Gene: Pm0188 / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q15KI8, EC: 2.4.99.4, EC: 2.4.99.6, EC: 2.4.99.9 #2: 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: 1.99 Å3/Da / Density % sol: 38.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.216 mM protein, 26% PEG3350, 0.1M NaCl, 0.4% Triton-X-100, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 3, 2005 / Details: Mar325 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→62.38 Å / Num. all: 87948 / Num. obs: 86251 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.069 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5305 / Rsym value: 0.308 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1183839.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.8488 Å2 / ksol: 0.350294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→43.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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