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- PDB-4phs: Selenomethionine substituted structure of domain of unknown funct... -

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Basic information

Entry
Database: PDB / ID: 4phs
TitleSelenomethionine substituted structure of domain of unknown function 1792 (DUF1792)
ComponentsPutative glycosyltransferase (GalT1)
KeywordsTRANSFERASE / streptococcal adhesin / glycosyltransferase / and DUF1792
Function / homologyGlycosyltransferase GT-D fold / Glycosyltransferase GT-D fold / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / transferase activity / nucleotide binding / URIDINE-5'-DIPHOSPHATE / Putative glycosyltransferase (GalT1)
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.54 Å
AuthorsZhang, H. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE017954-07 United States
CitationJournal: Nat Commun / Year: 2014
Title: The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold.
Authors: Zhang, H. / Zhu, F. / Yang, T. / Ding, L. / Zhou, M. / Li, J. / Haslam, S.M. / Dell, A. / Erlandsen, H. / Wu, H.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative glycosyltransferase (GalT1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7372
Polymers32,3331
Non-polymers4041
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.069, 44.596, 78.752
Angle α, β, γ (deg.)90.00, 110.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative glycosyltransferase (GalT1)


Mass: 32333.148 Da / Num. of mol.: 1 / Fragment: UNP residues 1-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Strain: FW213 / Gene: galT1, Spaf_1933
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I1ZPA1
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine 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 / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.82 Å3/Da / Density % sol: 32.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris, PEG 1500, NaAcetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97142, 0.97907, 0.97877
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971421
20.979071
30.978771
ReflectionResolution: 1.54→50 Å / Num. obs: 34221 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 33.1

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.2_1309) / Classification: refinement
RefinementResolution: 1.54→29.13 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.27 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1988 5.81 %
Rwork0.202 --
obs0.205 34221 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 25 234 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072336
X-RAY DIFFRACTIONf_angle_d1.2713156
X-RAY DIFFRACTIONf_dihedral_angle_d16.017875
X-RAY DIFFRACTIONf_chiral_restr0.087340
X-RAY DIFFRACTIONf_plane_restr0.005399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5403-1.57880.34051410.26942232X-RAY DIFFRACTION98
1.5788-1.62150.33721310.25282285X-RAY DIFFRACTION99
1.6215-1.66920.29921480.24082286X-RAY DIFFRACTION99
1.6692-1.72310.27131450.23082280X-RAY DIFFRACTION100
1.7231-1.78470.29091320.2352299X-RAY DIFFRACTION100
1.7847-1.85610.31831380.23242292X-RAY DIFFRACTION100
1.8561-1.94060.27621530.22792284X-RAY DIFFRACTION100
1.9406-2.04290.28111440.21852297X-RAY DIFFRACTION100
2.0429-2.17080.30741340.21432309X-RAY DIFFRACTION100
2.1708-2.33840.26221360.21192328X-RAY DIFFRACTION100
2.3384-2.57360.25541470.20632307X-RAY DIFFRACTION100
2.5736-2.94570.23331530.19922312X-RAY DIFFRACTION100
2.9457-3.710.19951360.17962347X-RAY DIFFRACTION100
3.71-29.13740.18931500.16092375X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.8741 Å / Origin y: 2.5594 Å / Origin z: 18.615 Å
111213212223313233
T0.0347 Å20.0032 Å2-0.0046 Å2-0.0479 Å20.0099 Å2--0.0356 Å2
L0.3023 °20.2308 °2-0.2529 °2-0.2651 °2-0.1659 °2--0.2535 °2
S-0.0091 Å °0.0621 Å °-0.0263 Å °-0.0053 Å °0.0322 Å °-0.0122 Å °-0.0178 Å °-0.0839 Å °0.0334 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESID -4:272)

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