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- PDB-3rhz: Structure and functional analysis of a new subfamily of glycosylt... -

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Basic information

Entry
Database: PDB / ID: 3rhz
TitleStructure and functional analysis of a new subfamily of glycosyltransferases required for glycosylation of serine-rich streptococcal adhesions
ComponentsNucleotide sugar synthetase-like protein
KeywordsTRANSFERASE / glycosyltransferase
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 / SAD / Resolution: 1.898 Å
AuthorsZhu, F. / Li, J. / 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
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 28, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2465
Polymers78,4022
Non-polymers8443
Water6,287349
1
A: Nucleotide sugar synthetase-like protein
B: Nucleotide sugar synthetase-like protein
hetero molecules

A: Nucleotide sugar synthetase-like protein
B: Nucleotide sugar synthetase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,49110
Polymers156,8044
Non-polymers1,6886
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area12840 Å2
ΔGint-80 kcal/mol
Surface area48910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.176, 193.862, 96.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-336-

HOH

31A-339-

HOH

41A-377-

HOH

51B-332-

HOH

61B-357-

HOH

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Components

#1: Protein Nucleotide sugar synthetase-like protein / Gtf3


Mass: 39200.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Gene: nss / Production host: Escherichia coli (E. coli) / References: UniProt: B5A7L9
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEG3350, 10% glycerol, 0.1 M succinic acid, 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: 0.97
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.898→30 Å / Num. all: 57280 / Num. obs: 57262 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.9 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_351)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.898→29.286 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2902 5.07 %RANDOM
Rwork0.1816 ---
obs0.1837 57235 99.84 %-
all-57280 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.334 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6978 Å2-0 Å2-0 Å2
2---2.9814 Å20 Å2
3----2.7164 Å2
Refinement stepCycle: LAST / Resolution: 1.898→29.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5327 0 51 349 5727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075493
X-RAY DIFFRACTIONf_angle_d1.1077446
X-RAY DIFFRACTIONf_dihedral_angle_d15.5432047
X-RAY DIFFRACTIONf_chiral_restr0.081819
X-RAY DIFFRACTIONf_plane_restr0.005943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8982-1.96610.29153040.24135303X-RAY DIFFRACTION99
1.9661-2.04480.25342950.20525368X-RAY DIFFRACTION100
2.0448-2.13780.26792870.1915352X-RAY DIFFRACTION100
2.1378-2.25050.25352620.18125411X-RAY DIFFRACTION100
2.2505-2.39140.22683170.1835362X-RAY DIFFRACTION100
2.3914-2.5760.25382670.18875464X-RAY DIFFRACTION100
2.576-2.8350.25512860.18785440X-RAY DIFFRACTION100
2.835-3.24480.21343090.18845435X-RAY DIFFRACTION100
3.2448-4.08630.20312870.16535501X-RAY DIFFRACTION100
4.0863-29.28910.17872880.16315697X-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)
10.1921-0.095-0.17320.33090.02750.45260.01760.00340.0315-0.0191-0.032-0.11670.01460.1433-0.00470.08690.02020.01110.1447-0.00020.1277-19.0194-13.242112.7025
20.9195-0.5450.28770.6934-0.05780.6771-0.1181-0.2851-0.13060.21630.1854-0.12260.3073-0.0793-0.12020.14450.095-0.0590.11690.040.036-26.4244-36.483243.1991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:328)
2X-RAY DIFFRACTION2(chain B and resid 2:328)

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