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- PDB-3e25: Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate ... -

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Basic information

Entry
Database: PDB / ID: 3.0E+25
TitleCrystal structure of M. tuberculosis glucosyl-3-phosphoglycerate synthase
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / glucosyltransferase / mycobacterial / GT81 UDP-glucose / 3-phosphoglycerate
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / UDP-alpha-D-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 / URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPereira, P.J.B. / Empadinhas, N. / Costa, M.S. / Macedo-Ribeiro, S.
Citation
Journal: Plos One / Year: 2008
Title: Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis
Authors: Pereira, P.J.B. / Empadinhas, N. / Albuquerque, L. / Sa-Moura, B. / da Costa, M.S. / Macedo-Ribeiro, S.
#1: Journal: Fems Microbiol.Lett. / Year: 2008
Title: Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase
Authors: Empadinhas, N. / Albuquerque, L. / Mendes, V. / Macedo-Ribeiro, S. / da Costa, M.S.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5534
Polymers35,9381
Non-polymers6153
Water1,53185
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1058
Polymers71,8762
Non-polymers1,2296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area5340 Å2
ΔGint-66 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.309, 100.309, 127.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Putative uncharacterized protein / glucosyl-3-phosphoglycerate synthase / GpgS


Mass: 35938.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1246, Rv1208 / Plasmid: pET30a / Production host: Escherichia coli (E. coli)
References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 4.45 Å3/Da / Density % sol: 72.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 0.5% polyethyleneglycol monomethyl ether 5000, 0.65M Na-K phosphate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC Q4R / Detector: CCD / Date: Jul 1, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→70.9 Å / Num. all: 17283 / Num. obs: 16855 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.069 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2481 / Rsym value: 0.33 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rubrobacter xylanophilus mannosyl-3-phosphoglycerate synthase (Sa-Moura et al., Acta Cryst. (2008). F64, 760-763)

Resolution: 2.7→32.335 Å / Occupancy max: 1 / Occupancy min: 0.66 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 814 5.15 %random
Rwork0.2036 14982 --
all0.2053 15796 --
obs0.2053 15796 91.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.422 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 115.71 Å2 / Biso mean: 45.122 Å2 / Biso min: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1-8.676 Å20 Å2-0 Å2
2--8.676 Å20 Å2
3----17.351 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 37 85 2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012134
X-RAY DIFFRACTIONf_angle_d1.412914
X-RAY DIFFRACTIONf_chiral_restr0.08343
X-RAY DIFFRACTIONf_plane_restr0.006369
X-RAY DIFFRACTIONf_dihedral_angle_d17.732806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.8690.3561130.2812260237383
2.869-3.0910.271240.2512403252788
3.091-3.4010.2651230.2292520264392
3.401-3.8930.2451650.1882571273696
3.893-4.9020.1731480.1582631277996
4.902-32.3370.2081410.1762597273894

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