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

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Basic information

Entry
Database: PDB / ID: 5jud
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with uridine-diphosphate (UDP) - GpgS*UDP
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase 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
URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium bovis AF2122/97 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 1.2Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0882
Polymers34,6841
Non-polymers4041
Water75742
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1754
Polymers69,3672
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area3960 Å2
ΔGint-33 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.240, 100.240, 125.620
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 Glucosyl-3-phosphoglycerate synthase


Mass: 34683.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis AF2122/97 (bacteria)
Gene: gpgS, Mb1240 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7U0E1, glucosyl-3-phosphoglycerate synthase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 4.55 Å3/Da / Density % sol: 72.96 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→50.12 Å / Num. obs: 19277 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05358 / Net I/σ(I): 19.98
Reflection shellResolution: 2.59→2.683 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7833 / Mean I/σ(I) obs: 2.59 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6N

4y6n


Resolution: 2.59→50.12 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 23.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1949 5.13 %Random selection
Rwork0.1948 ---
obs0.196 19277 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.03 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 25 42 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042181
X-RAY DIFFRACTIONf_angle_d1.122994
X-RAY DIFFRACTIONf_dihedral_angle_d17.473805
X-RAY DIFFRACTIONf_chiral_restr0.039361
X-RAY DIFFRACTIONf_plane_restr0.006383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5904-2.65510.32271320.28412560X-RAY DIFFRACTION99
2.6551-2.72690.27471550.25452564X-RAY DIFFRACTION100
2.7269-2.80720.22311290.22712594X-RAY DIFFRACTION99
2.8072-2.89770.28431270.22762554X-RAY DIFFRACTION99
2.8977-3.00130.22821430.21222583X-RAY DIFFRACTION100
3.0013-3.12150.21891280.21032547X-RAY DIFFRACTION100
3.1215-3.26350.25731330.21032609X-RAY DIFFRACTION100
3.2635-3.43550.23851520.21542555X-RAY DIFFRACTION100
3.4355-3.65070.18491280.1882616X-RAY DIFFRACTION100
3.6507-3.93250.22161590.18212537X-RAY DIFFRACTION100
3.9325-4.3280.19931240.16942591X-RAY DIFFRACTION100
4.328-4.95380.19351580.15632558X-RAY DIFFRACTION100
4.9538-6.23940.20691350.20672574X-RAY DIFFRACTION100
6.2394-50.12940.21631460.20122571X-RAY DIFFRACTION100

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