- PDB-2y4l: MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2y4l
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
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
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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 RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 202 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 202 TO ALA
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 CRYOPROTECTANT. MALONATE (MLI): 0.4 M NA MALONATE WAS THE PRECIPITATING AGENT USED DURING CRYSTALLIZATION. GUANOSINE-5'-DIPHOSPHATE (GDP): GDP IS THE NUCLEOTIDE PRODUCT FOLLOWING MGS CATALYZED MANNOSYL TRANSFER. MANGANESE (MN): 0.2 M MNCL2 WAS PRESENT IN THE MOTHER LIQUOR DURING CRYSTALLIZATION.
Sequence details
C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ...C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ENTROPY MINIMIZATION.
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Experimental details
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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
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.
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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22041
2530
5.1 %
RANDOM
Rwork
0.18762
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obs
0.1893
47314
99.85 %
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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