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

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Basic information

Entry
Database: PDB / ID: 5jqx
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with phosphoglyceric acid (PGA) - GpgS*PGA
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 / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 5, 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Glucosyl-3-phosphoglycerate synthase
C: Glucosyl-3-phosphoglycerate synthase
D: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4788
Polymers138,7344
Non-polymers7444
Water2,036113
1
A: Glucosyl-3-phosphoglycerate synthase
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7394
Polymers69,3672
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-34 kcal/mol
Surface area21400 Å2
MethodPISA
2
C: Glucosyl-3-phosphoglycerate synthase
hetero molecules

C: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7394
Polymers69,3672
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,y,-z1
Buried area3620 Å2
ΔGint-33 kcal/mol
Surface area21280 Å2
MethodPISA
3
D: Glucosyl-3-phosphoglycerate synthase
hetero molecules

D: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7394
Polymers69,3672
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3670 Å2
ΔGint-34 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.668, 128.180, 138.444
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glucosyl-3-phosphoglycerate synthase /


Mass: 34683.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: gpgS, Rv1208 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase
#2: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 4.43 Å3/Da / Density % sol: 72.26 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2014
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→44.504 Å / Num. obs: 58106 / % possible obs: 99.37 % / Redundancy: 3 % / Biso Wilson estimate: 67.53 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06619 / Net I/σ(I): 10.48
Reflection shellResolution: 2.82→2.921 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5487 / Mean I/σ(I) obs: 2.29 / % possible all: 99.09

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Processing

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

4dec


Resolution: 2.82→44.504 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 27.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2945 5.08 %random selection
Rwork0.2071 ---
obs0.2083 57926 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.3 Å2
Refinement stepCycle: LAST / Resolution: 2.82→44.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 44 113 8505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028608
X-RAY DIFFRACTIONf_angle_d0.63411776
X-RAY DIFFRACTIONf_dihedral_angle_d10.8533146
X-RAY DIFFRACTIONf_chiral_restr0.0231413
X-RAY DIFFRACTIONf_plane_restr0.0041516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.86620.37561130.33092630X-RAY DIFFRACTION99
2.8662-2.91570.34451420.32462589X-RAY DIFFRACTION99
2.9157-2.96870.33371360.30422616X-RAY DIFFRACTION99
2.9687-3.02570.30271580.29362568X-RAY DIFFRACTION99
3.0257-3.08750.28691410.2662615X-RAY DIFFRACTION99
3.0875-3.15460.3131500.27572650X-RAY DIFFRACTION99
3.1546-3.2280.30021500.26632537X-RAY DIFFRACTION99
3.228-3.30870.28071290.26152623X-RAY DIFFRACTION99
3.3087-3.39810.31261210.25152632X-RAY DIFFRACTION99
3.3981-3.49810.32271430.24312627X-RAY DIFFRACTION99
3.4981-3.61090.2578880.23022641X-RAY DIFFRACTION99
3.6109-3.73990.24371320.21282643X-RAY DIFFRACTION99
3.7399-3.88960.22061250.21422632X-RAY DIFFRACTION100
3.8896-4.06650.24581610.20562597X-RAY DIFFRACTION100
4.0665-4.28070.19841560.19022633X-RAY DIFFRACTION99
4.2807-4.54870.20411700.17772569X-RAY DIFFRACTION99
4.5487-4.89950.19591780.16472594X-RAY DIFFRACTION99
4.8995-5.39170.22511260.18382662X-RAY DIFFRACTION100
5.3917-6.17020.21371390.19292647X-RAY DIFFRACTION100
6.1702-7.7670.22261370.18472659X-RAY DIFFRACTION99
7.767-44.5090.14911500.16042617X-RAY DIFFRACTION97

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