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- PDB-5juc: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Basic information

Entry
Database: PDB / ID: 5juc
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgS*GPG*UDP*Mn2+_2
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
: / URIDINE-5'-DIPHOSPHATE / Chem-XDX / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlbesa-Jove, D. / Sancho-Vaello, E. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Guerin, M.E.
CitationJournal: Structure / Year: 2017
Title: Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS.
Authors: Albesa-Jove, D. / Romero-Garcia, J. / Sancho-Vaello, E. / Contreras, F.X. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Biarnes, X. / Planas, A. / Guerin, M.E.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water52229
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_655-x+1,-y,z1
Buried area5340 Å2
ΔGint-34 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.434, 99.434, 126.785
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 / Sugars , 2 types, 2 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase
#5: Sugar ChemComp-XDX / (2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid / (2R)-2-(alpha-D-glucosyloxy)-3-(phosphonooxy)propanoic acid / (2R)-2-(D-glucosyloxy)-3-(phosphonooxy)propanoic acid / (2R)-2-(glucosyloxy)-3-(phosphonooxy)propanoic acid


Type: D-saccharide / Mass: 348.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17O12P

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Non-polymers , 4 types, 33 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: 0.97933 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.55→70.32 Å / Num. obs: 20094 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1158 / Net I/σ(I): 7.94
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.15 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6N

4y6n


Resolution: 2.8→70.31 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 781 5.15 %Random selection
Rwork0.1908 ---
obs0.1921 15156 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→70.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 56 29 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062186
X-RAY DIFFRACTIONf_angle_d0.7342982
X-RAY DIFFRACTIONf_dihedral_angle_d15.6431319
X-RAY DIFFRACTIONf_chiral_restr0.045361
X-RAY DIFFRACTIONf_plane_restr0.006384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.97560.3231420.27652385X-RAY DIFFRACTION99
2.9756-3.20540.27391590.24122334X-RAY DIFFRACTION99
3.2054-3.52790.26411430.21772384X-RAY DIFFRACTION100
3.5279-4.03840.19571150.18532391X-RAY DIFFRACTION100
4.0384-5.08770.194950.1542434X-RAY DIFFRACTION100
5.0877-70.33240.18541270.1852447X-RAY DIFFRACTION100

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