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- PDB-4y9x: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Basic information

Entry
Database: PDB / ID: 4y9x
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-3
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-alpha-D-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: 2.637 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 17, 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)35,7138
Polymers34,6841
Non-polymers1,0297
Water1,17165
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,42516
Polymers69,3672
Non-polymers2,05814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area7380 Å2
ΔGint-57 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.850, 98.850, 127.790
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 (strain ATCC 25618 / H37Rv) (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 , 6 types, 72 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


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


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.5 Å3/Da / Density % sol: 72.67 %
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 / Detector: PIXEL / Date: May 23, 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: 2.637→29.06 Å / Num. obs: 18052 / % possible obs: 99.86 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.39
Reflection shellResolution: 2.637→2.732 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.573 / % possible all: 98.94

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DEC

4dec


Resolution: 2.637→29.06 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 912 5.05 %random selection
Rwork0.2141 ---
obs0.2161 18042 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.637→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 61 65 2235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042268
X-RAY DIFFRACTIONf_angle_d1.1153129
X-RAY DIFFRACTIONf_dihedral_angle_d15.169844
X-RAY DIFFRACTIONf_chiral_restr0.038372
X-RAY DIFFRACTIONf_plane_restr0.007393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6375-2.77640.32521370.28462404X-RAY DIFFRACTION99
2.7764-2.95020.34541240.23542442X-RAY DIFFRACTION100
2.9502-3.17780.26111280.22082456X-RAY DIFFRACTION100
3.1778-3.49710.26641220.21512432X-RAY DIFFRACTION100
3.4971-4.0020.26331470.20012442X-RAY DIFFRACTION100
4.002-5.03780.21011210.22469X-RAY DIFFRACTION100
5.0378-29.05810.25231330.22152485X-RAY DIFFRACTION100

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