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- PDB-3qkw: Structure of Streptococcus parasangunini Gtf3 glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 3qkw
TitleStructure of Streptococcus parasangunini Gtf3 glycosyltransferase
ComponentsNucleotide sugar synthetase-like protein
KeywordsTRANSFERASE / GT-B fold / glycosyltransferase / NUCLEOTIDE SUGAR SYNTHETASE-LIKE PROTEIN
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / protein glycosylation / nucleotide binding
Similarity search - Function
Glucosyltransferase 3 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glucosyltransferase 3
Similarity search - Component
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.287 Å
AuthorsZhu, F. / Erlandsen, H. / Huang, Y. / Ding, L. / Zhou, M. / Liang, X. / Ma, J.-B. / Wu, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Analysis of a New Subfamily of Glycosyltransferases Required for Glycosylation of Serine-rich Streptococcal Adhesins.
Authors: Zhu, F. / Erlandsen, H. / Ding, L. / Li, J. / Huang, Y. / Zhou, M. / Liang, X. / Ma, J. / Wu, H.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 21, 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotide sugar synthetase-like protein
B: Nucleotide sugar synthetase-like protein
C: Nucleotide sugar synthetase-like protein
D: Nucleotide sugar synthetase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6888
Polymers153,0724
Non-polymers1,6174
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-72 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.217, 99.244, 188.185
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
Nucleotide sugar synthetase-like protein


Mass: 38267.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Gene: nss / Plasmid: pET-SUMO-Gtf3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: B5A7L9
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 ul of protein solution (15 mg/ml protein and 10mM UDP-Glucose) was mixed with 1 ul of reservoir (0.1M Succinic Acid, 11% Polyethylene glycol 3,350, 10% glycerol), pH 7.0, VAPOR DIFFUSION, ...Details: 1 ul of protein solution (15 mg/ml protein and 10mM UDP-Glucose) was mixed with 1 ul of reservoir (0.1M Succinic Acid, 11% Polyethylene glycol 3,350, 10% glycerol), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: Double crystal - liquid nitrogen cooled / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→42.512 Å / Num. obs: 63229 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 10.8 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_351)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A SAD dataset was collected using Se-Met crystal. Initial structure determined in spacegroup C2221 with Gtf3 dimer.

Resolution: 2.287→42.512 Å / SU ML: 0.37 / Isotropic thermal model: Anisotropic / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 3217 5.09 %
Rwork0.187 --
obs0.1901 63229 95.69 %
all-63229 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.737 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6213 Å2-0 Å2-0 Å2
2---5.2667 Å20 Å2
3----7.3547 Å2
Refinement stepCycle: LAST / Resolution: 2.287→42.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10583 0 100 188 10871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810987
X-RAY DIFFRACTIONf_angle_d1.14514894
X-RAY DIFFRACTIONf_dihedral_angle_d17.214090
X-RAY DIFFRACTIONf_chiral_restr0.0771637
X-RAY DIFFRACTIONf_plane_restr0.0051888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.287-2.36920.3472720.25945227X-RAY DIFFRACTION85
2.3692-2.46410.33493020.23855590X-RAY DIFFRACTION90
2.4641-2.57620.33243260.23455850X-RAY DIFFRACTION94
2.5762-2.7120.30973290.2275922X-RAY DIFFRACTION96
2.712-2.88190.29423140.22025981X-RAY DIFFRACTION96
2.8819-3.10440.30643070.22276127X-RAY DIFFRACTION97
3.1044-3.41660.2723170.20286184X-RAY DIFFRACTION99
3.4166-3.91070.22733540.16626253X-RAY DIFFRACTION99
3.9107-4.9260.19913290.14176321X-RAY DIFFRACTION100
4.926-42.51880.19463670.15846557X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3872-0.1982-0.12840.6585-0.04110.4673-0.00720.0158-0.02480.00210.09870.16650.0122-0.05710.25560.1849-0.00580.00990.25440.03190.2555-20.197811.8655-35.7629
20.6955-0.32210.39910.4889-0.1320.37390.01780.075-0.02360.05440.0426-0.0429-0.01270.09240.14860.18370.0078-0.03060.192-0.01780.178118.1814-10.7748-32.9353
30.4396-0.23620.18530.5331-0.10790.2641-0.0982-0.16520.14350.4330.0529-0.1419-0.18780.00910.00010.44250.0058-0.09670.2146-0.06680.22729.744719.1676-10.6127
40.4544-0.40270.06450.6507-0.17320.3218-0.089-0.1686-0.19880.29910.1460.24680.0671-0.1099-00.3524-0.02390.10180.28590.07720.3139-14.9586-18.1143-12.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:329)
2X-RAY DIFFRACTION2(CHAIN B AND RESID -1:329)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 0:330)
4X-RAY DIFFRACTION4(CHAIN D AND RESID -1:329)

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