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- PDB-4y6n: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Basic information

Entry
Database: PDB / ID: 4y6n
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and phosphoglyceric acid (PGA) - GpgS Mn2+ UDP-Glc PGA-1
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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
3-PHOSPHOGLYCERIC ACID / : / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsAlbesa-Jove, D. / Rodrigo-Unzueta, A. / Cifuente, J.O. / Urresti, S. / Comino, N. / Sancho-Vaello, E. / Guerin, M.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase.
Authors: Albesa-Jove, D. / Mendoza, F. / Rodrigo-Unzueta, A. / Gomollon-Bel, F. / Cifuente, J.O. / Urresti, S. / Comino, N. / Gomez, H. / Romero-Garcia, J. / Lluch, J.M. / Sancho-Vaello, E. / ...Authors: Albesa-Jove, D. / Mendoza, F. / Rodrigo-Unzueta, A. / Gomollon-Bel, F. / Cifuente, J.O. / Urresti, S. / Comino, N. / Gomez, H. / Romero-Garcia, J. / Lluch, J.M. / Sancho-Vaello, E. / Biarnes, X. / Planas, A. / Merino, P. / Masgrau, L. / Guerin, M.E.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Structure summary
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6156
Polymers34,6841
Non-polymers9315
Water64936
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,23012
Polymers69,3672
Non-polymers1,86310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area6770 Å2
ΔGint-53 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.730, 98.730, 127.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucosyl-3-phosphoglycerate synthase /


Mass: 34683.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gpgS, Rv1208 / Plasmid: pET29a::GSGA-Rv1208 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14% PEG 8,000, 0.3-0.5 M Li sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 22, 2013
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.348→29.01 Å / Num. obs: 25437 / % possible obs: 99.77 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.54
Reflection shellResolution: 2.348→2.432 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.5 / % possible all: 97.87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DEC

4dec


Resolution: 2.348→29.009 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1307 5.15 %random selection
Rwork0.1731 ---
obs0.1744 25392 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.348→29.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 56 36 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132239
X-RAY DIFFRACTIONf_angle_d1.3143067
X-RAY DIFFRACTIONf_dihedral_angle_d15.401827
X-RAY DIFFRACTIONf_chiral_restr0.07367
X-RAY DIFFRACTIONf_plane_restr0.007388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3478-2.44170.33941470.29092620X-RAY DIFFRACTION98
2.4417-2.55280.28481460.24632675X-RAY DIFFRACTION100
2.5528-2.68730.21541420.20122656X-RAY DIFFRACTION100
2.6873-2.85550.21441480.19192639X-RAY DIFFRACTION100
2.8555-3.07580.27171400.19812699X-RAY DIFFRACTION100
3.0758-3.38490.21291450.20662684X-RAY DIFFRACTION100
3.3849-3.87370.20311380.17462688X-RAY DIFFRACTION100
3.8737-4.87670.19251420.15722700X-RAY DIFFRACTION100
4.8767-29.0110.17771590.15852724X-RAY DIFFRACTION100

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