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Yorodumi- PDB-2ex1: Crystal structure of mutifunctional sialyltransferase from Pasteu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ex1 | ||||||
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Title | Crystal structure of mutifunctional sialyltransferase from Pasteurella multocida with CMP bound | ||||||
Components | a2,3-sialyltransferase, a2,a6-sialyltransferase | ||||||
Keywords | TRANSFERASE / two Rossman fold sialyltransferase-CMP complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pasteurella multocida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 sequence database available for the protein |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ex1.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ex1.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ex1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2ex1 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2ex1 | HTTPS FTP |
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-Related structure data
Related structure data | 2ex0C 1ex0S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 46236.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein has four enzymatic activites / 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 |
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#2: Chemical | ChemComp-C5P / |
#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: 2.74 Å3/Da / Density % sol: 55.13 % |
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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, 2 mM CMP-sialic acid, 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: 0.97931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 22, 2005 / Details: Mar325 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2→64.15 Å / Num. all: 33988 / Num. obs: 33403 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.059 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2457 / Rsym value: 0.24 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EX0 Resolution: 2→38.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1277163.39 / 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: 59.2631 Å2 / ksol: 0.3773 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→38.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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