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- PDB-4y6u: Mycobacterial protein -

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Basic information

Entry
Database: PDB / ID: 4y6u
TitleMycobacterial protein
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: 2.271 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7138
Polymers34,6841
Non-polymers1,0297
Water1,874104
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_655-x+1,-y,z1
Buried area7400 Å2
ΔGint-57 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.280, 99.280, 128.230
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, 111 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.: 104 / 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: 4.56 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14% PEG 8000, 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 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: 2.271→70.2 Å / Num. obs: 52965 / % possible obs: 99.28 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.68
Reflection shellResolution: 2.271→2.352 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.479 / % possible all: 98.78

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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: 2.271→70.202 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2677 5.05 %random selection
Rwork0.1841 ---
obs0.1856 52965 93.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.271→70.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 61 104 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132239
X-RAY DIFFRACTIONf_angle_d1.3843065
X-RAY DIFFRACTIONf_dihedral_angle_d15.46833
X-RAY DIFFRACTIONf_chiral_restr0.054364
X-RAY DIFFRACTIONf_plane_restr0.008386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2711-2.31240.32431370.27812485X-RAY DIFFRACTION89
2.3124-2.35690.33111320.25142600X-RAY DIFFRACTION92
2.3569-2.4050.25141450.23872600X-RAY DIFFRACTION94
2.405-2.45730.26141300.23092717X-RAY DIFFRACTION94
2.4573-2.51450.30281340.2262632X-RAY DIFFRACTION94
2.5145-2.57740.26181060.20922692X-RAY DIFFRACTION94
2.5774-2.64710.23771510.19342682X-RAY DIFFRACTION94
2.6471-2.7250.26431550.18872638X-RAY DIFFRACTION94
2.725-2.81290.21931470.17882650X-RAY DIFFRACTION94
2.8129-2.91350.25081490.19162649X-RAY DIFFRACTION94
2.9135-3.03010.19741410.1852669X-RAY DIFFRACTION94
3.0301-3.1680.21621590.19412634X-RAY DIFFRACTION94
3.168-3.3350.21771590.20122639X-RAY DIFFRACTION94
3.335-3.5440.22131490.1822645X-RAY DIFFRACTION94
3.544-3.81760.20091150.17442676X-RAY DIFFRACTION94
3.8176-4.20170.20311330.16942641X-RAY DIFFRACTION94
4.2017-4.80960.18241530.15632681X-RAY DIFFRACTION95
4.8096-6.05910.19451600.17762675X-RAY DIFFRACTION95
6.0591-70.23510.18651220.18122683X-RAY DIFFRACTION95

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