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- PDB-4y7f: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Basic information

Entry
Database: PDB / ID: 4y7f
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and 3-(phosphonooxy)propanoic acid (PPA) - GpgS Mn2+ UDP-Glc PPA
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-(phosphonooxy)propanoic acid / : / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.231 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 14, 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)35,6336
Polymers34,6841
Non-polymers9495
Water57632
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,26612
Polymers69,3672
Non-polymers1,89910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5740 Å2
ΔGint-71 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.940, 97.940, 126.780
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 / GpgS


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, 37 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-48X / 3-(phosphonooxy)propanoic acid


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 4.38 Å3/Da / Density % sol: 71.94 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 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: 3.23→69.25 Å / Num. obs: 9590 / % possible obs: 99.66 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.97
Reflection shellResolution: 3.23→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.5 / % possible all: 99.69

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DEC

4dec


Resolution: 3.231→69.25 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 903 4.8 %random selection
Rwork0.1699 ---
obs0.1717 9590 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.231→69.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 56 32 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112216
X-RAY DIFFRACTIONf_angle_d1.3053040
X-RAY DIFFRACTIONf_dihedral_angle_d15.345817
X-RAY DIFFRACTIONf_chiral_restr0.044362
X-RAY DIFFRACTIONf_plane_restr0.01383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2308-3.43320.32371430.29612956X-RAY DIFFRACTION99
3.4332-3.69830.2251620.20782967X-RAY DIFFRACTION100
3.6983-4.07040.24561490.18343039X-RAY DIFFRACTION100
4.0704-4.65930.17911510.13782970X-RAY DIFFRACTION100
4.6593-5.86970.17641460.15253001X-RAY DIFFRACTION100
5.8697-69.26990.21520.15422983X-RAY DIFFRACTION100

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