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

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Basic information

Entry
Database: PDB / ID: 4dec
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and phosphoglyceric acid (PGA)
ComponentsGLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / glycosyltransferase activity / magnesium ion binding / protein homodimerization activity / metal ion binding
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 / : / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsAlbesa-Jove, D. / Urresti, S. / van der Woerd, M. / Guerin, M.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria.
Authors: Urresti, S. / Albesa-Jove, D. / Schaeffer, F. / Pham, H.T. / Kaur, D. / Gest, P. / van der Woerd, M.J. / Carreras-Gonzalez, A. / Lopez-Fernandez, S. / Alzari, P.M. / Brennan, P.J. / Jackson, M. / Guerin, M.E.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5107
Polymers36,5831
Non-polymers9276
Water3,909217
1
A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules

A: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,02014
Polymers73,1652
Non-polymers1,85412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area7320 Å2
ΔGint-85 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.316, 100.316, 127.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)


Mass: 36582.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgS, MT1246, Rv1208 / Plasmid: pET28a-gpgS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 6 types, 223 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM UDP, 5mM 3PG, 5mM MnCl2, Tris-HCL pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.98→39.36 Å / Num. all: 43786 / Num. obs: 42409 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.71 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.4
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.02 / Num. unique all: 6950 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→39.36 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.853 / SU ML: 0.55 / σ(F): 2.01 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1946 4.59 %
Rwork0.1772 --
obs0.1785 42399 96.84 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.412 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 109.08 Å2 / Biso mean: 41.9334 Å2 / Biso min: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1-7.3863 Å20 Å2-0 Å2
2--7.3863 Å20 Å2
3----14.7726 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 53 217 2405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182261
X-RAY DIFFRACTIONf_angle_d1.5663105
X-RAY DIFFRACTIONf_chiral_restr0.11370
X-RAY DIFFRACTIONf_plane_restr0.008394
X-RAY DIFFRACTIONf_dihedral_angle_d14.191837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9778-2.02730.32331380.30872896303497
2.0273-2.08210.32081380.267629563094100
2.0821-2.14330.28641420.250129533095100
2.1433-2.21250.26931460.222530003146100
2.2125-2.29160.22181390.19872914305399
2.2916-2.38330.23431400.1872949308998
2.3833-2.49180.26261370.19822904304198
2.4918-2.62310.20691410.19482899304098
2.6231-2.78740.21631400.17772900304097
2.7874-3.00260.21721410.17842854299596
3.0026-3.30460.21251320.18052848298095
3.3046-3.78250.19371430.16262804294795
3.7825-4.76420.15431340.13632840297494
4.7642-39.37110.1781350.16162736287191

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