+Open data
-Basic information
Entry | Database: PDB / ID: 2y4m | |||||||||
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Title | MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH GDP-Mannose | |||||||||
Components | MANNOSYLGLYCERATE SYNTHASE | |||||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / GT FAMILY 78 MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE / GDP-MANNOSE | |||||||||
Function / homology | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / metal ion binding / Alpha Beta / Chem-GDX / Mannosylglycerate synthase Function and homology information | |||||||||
Biological species | RHODOTHERMUS MARINUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 2y4m.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4m.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4m ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4m | HTTPS FTP |
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-Related structure data
Related structure data | 2y4jC 2y4kC 2y4lC 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: D0MI02, mannosyl-3-phosphoglycerate synthase |
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-Non-polymers , 5 types, 177 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 B, GLN 201 TO ALA ...ENGINEERED |
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Nonpolymer details | ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYOPROTECTANT GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE 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: 5.58 Å3/Da / Density % sol: 78 % / 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, 0.3 M MAGNESIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2009 / Details: OSMIC VARIMAX HF MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→23.4 Å / Num. obs: 47729 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 47.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BO7 Resolution: 2.7→129.47 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.432 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.219 / 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: 40.369 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→129.47 Å
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Refine LS restraints |
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