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- PDB-5e9t: Crystal structure of GtfA/B complex -

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Basic information

Entry
Database: PDB / ID: 5e9t
TitleCrystal structure of GtfA/B complex
Components
  • Glycosyltransferase Gtf1
  • Glycosyltransferase-stabilizing protein Gtf2
KeywordsTRANSFERASE/CHAPERONE / Glycosyltransferase / Accessory protein translocation / Complex / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


: / protein N-acetylglucosaminyltransferase complex / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / regulation of protein stability / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Glycosyltransferase-stabilising protein GtfB / Glycosyltransferase GtfA / : / GtfA extended beta-sheet domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase stabilizing protein GtfB / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsChen, Y. / Rapoport, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein.
Authors: Chen, Y. / Seepersaud, R. / Bensing, B.A. / Sullam, P.M. / Rapoport, T.A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.5Sep 27, 2023Group: 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase Gtf1
B: Glycosyltransferase-stabilizing protein Gtf2
C: Glycosyltransferase Gtf1
D: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,1196
Polymers220,0704
Non-polymers492
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-41 kcal/mol
Surface area80600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.930, 196.410, 220.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Glycosyltransferase Gtf1 / Glycosyltransferase GtfA


Mass: 58399.207 Da / Num. of mol.: 2 / Mutation: S124F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf1, gtfA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AET5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein Glycosyltransferase-stabilizing protein Gtf2 / Glycosyltransferase chaperone GtfB / orf4


Mass: 51635.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf2, gtfB / Production host: Escherichia coli (E. coli) / References: UniProt: Q79T00
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG4000, magnesium chloride, Tris / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.92→122.123 Å / Num. obs: 73613 / % possible obs: 99.9 % / Redundancy: 58.9 % / Biso Wilson estimate: 35.41 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.239 / Rrim(I) all: 0.312 / Χ2: 1.029 / Net I/σ(I): 23.13 / Num. measured all: 5781655
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. measured obsNum. possibleNum. unique obs% possible allRmerge F obsMean I/σ(I) obsRmerge(I) obsRrim(I) all
2.92-360.9984058208752699.9
2.6-2.672016998012799399.80.0580.2
2.67-2.753374747789778399.90.2110.59
2.75-2.834061207594758999.90.420.93
2.83-2.934366887336732699.90.661.417.777.835
2.93-3.034327167111710399.90.8012.015.2815.325
3.03-3.14417074685968581000.9053.043.3133.341
3.14-3.27401320660266011000.9524.652.1482.166
3.27-3.42384868634363431000.9837.141.3861.397
3.42-3.59366002605560531000.99310.870.8470.854
3.59-3.78350451580458031000.99715.730.5490.554
3.78-4.01329193548754861000.99820.990.3620.365
4.01-4.29306794514451441000.99928.340.2290.231
4.29-4.63283788481748171000.99937.990.1470.148
4.63-5.07257774443544341000.99943.40.120.121
5.07-5.67231834402640261000.99942.380.1260.127
5.67-6.55199425357435741000.99945.890.1140.115
6.55-8.02160284304430441000.99954.820.0860.087
8.02-11.3411927223972396100175.290.060.061
11.34-122.1604741385136398.40.99977.620.0550.056

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD
Starting model: 4PQG

4pqg


Resolution: 2.92→122.123 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.275 3569 4.85 %
Rwork0.217 70024 -
obs0.2199 73593 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 433.16 Å2 / Biso mean: 68.2429 Å2 / Biso min: 4.05 Å2
Refinement stepCycle: final / Resolution: 2.92→122.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15438 0 2 34 15474
Biso mean--17.61 33.14 -
Num. residues----1898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115782
X-RAY DIFFRACTIONf_angle_d1.34621396
X-RAY DIFFRACTIONf_chiral_restr0.0692322
X-RAY DIFFRACTIONf_plane_restr0.0072804
X-RAY DIFFRACTIONf_dihedral_angle_d17.8859404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.92-2.960.35951380.312127512889100
2.96-3.00230.35181420.319628012943100
3.0023-3.04710.38511610.318427412902100
3.0471-3.09480.35331440.298727852929100
3.0948-3.14550.37591320.298427812913100
3.1455-3.19970.36961270.282927642891100
3.1997-3.25790.28141160.268128272943100
3.2579-3.32060.30911700.255727392909100
3.3206-3.38840.33441420.242627962938100
3.3884-3.46210.26681520.224527542906100
3.4621-3.54260.25931280.212628012929100
3.5426-3.63120.29161460.217228072953100
3.6312-3.72940.28541430.207927662909100
3.7294-3.83910.28881450.202327662911100
3.8391-3.96310.2491580.19527832941100
3.9631-4.10470.2551540.192427932947100
4.1047-4.26910.22571420.177327992941100
4.2691-4.46340.23021380.168728062944100
4.4634-4.69870.20461190.157428262945100
4.6987-4.99310.24791620.160427792941100
4.9931-5.37860.24351240.181728622986100
5.3786-5.91990.26841490.19528202969100
5.9199-6.77640.2791400.203728522992100
6.7764-8.53730.25071470.206328683015100
8.5373-122.23030.22591500.21882957310799

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