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- PDB-4pqg: Crystal structure of the pneumococcal O-GlcNAc transferase GtfA i... -

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Basic information

Entry
Database: PDB / ID: 4pqg
TitleCrystal structure of the pneumococcal O-GlcNAc transferase GtfA in complex with UDP and GlcNAc
ComponentsGlycosyltransferase Gtf1
KeywordsTRANSFERASE / O-GlcNAc transferase / GT-B fold / Rossmann fold / GtfB
Function / homology
Function and homology information


protein O-linked glycosylation via serine / protein N-acetylglucosaminyltransferase complex / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Glycosyltransferase GtfA / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShi, W.W. / Jiang, Y.L. / Zhu, F. / Yang, Y.H. / Wu, H. / Ren, Y.M. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of a Novel O-Linked N-Acetyl-d-glucosamine (O-GlcNAc) Transferase, GtfA, Reveals Insights into the Glycosylation of Pneumococcal Serine-rich Repeat Adhesins.
Authors: Shi, W.W. / Jiang, Y.L. / Zhu, F. / Yang, Y.H. / Shao, Q.Y. / Yang, H.B. / Ren, Y.M. / Wu, H. / Chen, Y. / Zhou, C.Z.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Glycosyltransferase Gtf1
B: Glycosyltransferase Gtf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9706
Polymers117,7192
Non-polymers1,2514
Water12,016667
1
A: Glycosyltransferase Gtf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4853
Polymers58,8601
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase Gtf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4853
Polymers58,8601
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glycosyltransferase Gtf1
hetero molecules

B: Glycosyltransferase Gtf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9706
Polymers117,7192
Non-polymers1,2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area4680 Å2
ΔGint-22 kcal/mol
Surface area42660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.240, 125.630, 127.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyltransferase Gtf1


Mass: 58859.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: gtf1, SP_1758 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97P84, UniProt: A0A0H2URG7*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-Cl, 0.2 M Li2SO4, 15% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2→47.41 Å / Num. obs: 77663 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.093 / Net I/σ(I): 17
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 / Num. unique all: 11169 / Rsym value: 0.428 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→47.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.589 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24819 3906 5 %RANDOM
Rwork0.19863 ---
obs0.20116 73684 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.863 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20 Å2
2---2.24 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 80 667 8937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.94611481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9751005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82324.921445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.428151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9621530
X-RAY DIFFRACTIONr_chiral_restr0.0930.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 264 -
Rwork0.24 5041 -
obs--99.76 %

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