+Open data
-Basic information
Entry | Database: PDB / ID: 2y4l | |||||||||
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Title | MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP | |||||||||
Components | MANNOSYLGLYCERATE SYNTHASE | |||||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE | |||||||||
Function / homology | Function and homology information mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | RHODOTHERMUS MARINUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Davis, B.G. / Davies, G.J. / Gilbert, H.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase. Authors: Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Dumon, C. / Davis, B.G. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y4l.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4l.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4l ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4l | HTTPS FTP |
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-Related structure data
Related structure data | 2y4jC 2y4kC 2y4mC 2bo7S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44600.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-382 / Mutation: YES Source method: isolated from a genetically manipulated source Details: C-TERMINAL TRUNCATION OF LAST 15 RESIDUES / Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: DSM 4252 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER References: UniProt: Q9RFR0, UniProt: D0MI02*PLUS, mannosyl-3-phosphoglycerate synthase |
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-Non-polymers , 5 types, 116 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 202 TO ALA ...ENGINEERED |
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Nonpolymer details | ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYSTAL CRYOPROTECTANT. MALONATE (MLI): 0.4 M NA ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYSTAL CRYOPROTEC |
Sequence details | C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ...C-TERMINAL TRUNCATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.61 Å3/Da / Density % sol: 78.1 % / Description: NONE |
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Crystal grow | pH: 5 Details: 4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE PH 5.5, 0.2 MNCL2, 0.4 M SODIUM MALONATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9789 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 47314 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BO7 Resolution: 2.8→129.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.501 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 48.073 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→129.69 Å
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