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- PDB-6mw5: UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase with b... -

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Basic information

Entry
Database: PDB / ID: 6mw5
TitleUDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase with bound UDP and Platinum
ComponentsUDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GT-A fold
Function / homologyGlycosyl transferase, family 8 / Glycosyl transferase family 8 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / : / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase family 8 protein
Function and homology information
Biological speciesPythium ultimum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, H.W. / Wood, Z.A. / West, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM084383 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A terminal alpha 3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii .
Authors: Mandalasi, M. / Kim, H.W. / Thieker, D. / Sheikh, M.O. / Gas-Pascual, E. / Rahman, K. / Zhao, P. / Daniel, N.G. / van der Wel, H. / Ichikawa, H.T. / Glushka, J.N. / Wells, L. / Woods, R.J. / ...Authors: Mandalasi, M. / Kim, H.W. / Thieker, D. / Sheikh, M.O. / Gas-Pascual, E. / Rahman, K. / Zhao, P. / Daniel, N.G. / van der Wel, H. / Ichikawa, H.T. / Glushka, J.N. / Wells, L. / Woods, R.J. / Wood, Z.A. / West, C.M.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: 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: UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7674
Polymers30,1051
Non-polymers6613
Water97354
1
A: UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase
hetero molecules

A: UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5338
Polymers60,2102
Non-polymers1,3236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4120 Å2
ΔGint-76 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.780, 83.780, 75.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-427-

HOH

31A-453-

HOH

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Components

#1: Protein UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase


Mass: 30105.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pythium ultimum (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: K3WC47, N-acetyllactosaminide 3-alpha-galactosyltransferase
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 8-12% PEG4000, 0.4M ammonium sulfate, 0.1M sodium acetate
PH range: 4.0-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.85 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2.1→46.7 Å / Num. obs: 29424 / % possible obs: 97.4 % / Redundancy: 13.5 % / Biso Wilson estimate: 45.2 Å2 / Net I/σ(I): 28.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.2 % / Num. unique obs: 2114 / % possible all: 94.8

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHENIX(1.13_2998)phasing
PHENIX(1.13_2998)refinement
Coot0.8.6.1model building
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.686 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.2419 1476 5.03 %
Rwork0.196 --
obs0.1983 29359 97.48 %
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 30 54 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062013
X-RAY DIFFRACTIONf_angle_d0.7862743
X-RAY DIFFRACTIONf_dihedral_angle_d13.253711
X-RAY DIFFRACTIONf_chiral_restr0.053293
X-RAY DIFFRACTIONf_plane_restr0.006345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1680.41651290.35062530X-RAY DIFFRACTION97
2.168-2.24550.46521220.35482266X-RAY DIFFRACTION88
2.2455-2.33540.53671240.43222282X-RAY DIFFRACTION88
2.3354-2.44170.28331370.2292601X-RAY DIFFRACTION100
2.4417-2.57040.2661420.20322601X-RAY DIFFRACTION100
2.5704-2.73140.23181380.18622588X-RAY DIFFRACTION100
2.7314-2.94230.25611330.18852616X-RAY DIFFRACTION100
2.9423-3.23830.22931330.18742607X-RAY DIFFRACTION100
3.2383-3.70670.25071370.17462598X-RAY DIFFRACTION100
3.7067-4.66940.19021420.14982592X-RAY DIFFRACTION100
4.6694-46.69780.17471390.17252602X-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)
10.9163-0.5645-0.2271.473-0.40671.1112-0.1301-0.37690.23560.9980.03050.0789-0.3512-0.0275-0.12640.39970.01160.07990.1993-0.02670.25522.618838.837124.5716
21.27530.5343-0.0661.05-0.94711.08590.3345-0.57960.26611.097-0.37180.1718-0.23630.07180.07290.90970.12320.04630.3717-0.14590.20422.582344.497533.3115
30.7877-0.7476-0.06421.5130.76780.6681-0.2078-0.7817-0.36761.30460.29540.12310.6145-0.34060.36420.67850.0430.21650.26840.02250.210922.388529.06926.9659
40.4061-0.49590.01650.6777-0.34340.6668-0.18060.18740.10660.12520.1216-0.01220.0813-0.0922-0.00210.2773-0.04540.08090.2545-0.02010.294521.945931.139811.3741
50.65960.29640.18560.25540.13250.3464-0.23010.0931-0.30360.36830.1124-0.15820.48940.044-0.02320.5512-0.01430.10460.21280.01660.318426.899720.003419.7563
60.9277-0.28371.53370.2533-0.6162.7357-0.44750.0621-0.1568-0.1768-0.0402-0.66520.22471.1283-0.12470.39440.03970.11980.3888-0.00690.472836.5921.886914.2516
70.55160.0516-0.21180.2731-0.13470.1189-0.09880.3267-0.0318-0.2352-0.0780.19940.1967-0.2949-0.1130.3608-0.08920.11740.2079-0.05470.277624.095425.5995.7831
80.38610.0379-0.47850.81520.02580.47390.08920.28230.1903-0.01620.0461-0.1974-0.3210.15160.00530.347-0.08210.05560.36210.00430.388930.312843.43866.1702
90.3165-0.13880.50620.0785-0.43743.08770.11-0.03540.21960.13570.1859-0.0815-0.6789-0.41280.11440.5477-0.03230.15240.1720.00220.435623.497552.159819.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 170 )
6X-RAY DIFFRACTION6chain 'A' and (resid 171 through 186 )
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 206 )
8X-RAY DIFFRACTION8chain 'A' and (resid 207 through 246 )
9X-RAY DIFFRACTION9chain 'A' and (resid 247 through 266 )

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