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- PDB-6mw8: UDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase with b... -

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Basic information

Entry
Database: PDB / ID: 6mw8
TitleUDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase with bound UDP and Manganese
ComponentsUDP-galactose:glucoside-Skp1 alpha-D-galactosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GT-A fold
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETATE ION / : / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase family 8 protein
Similarity search - Component
Biological speciesPythium ultimum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,8047
Polymers30,1051
Non-polymers6986
Water2,162120
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)61,60714
Polymers60,2102
Non-polymers1,39712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5120 Å2
ΔGint-43 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.055, 84.055, 76.076
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-421-

HOH

21A-429-

HOH

31A-471-

HOH

41A-513-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.25 Å3/Da / Density % sol: 45 %
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 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 Å / Relative weight: 1
ReflectionResolution: 1.75→37.591 Å / Num. obs: 28125 / % possible obs: 99.9 % / Redundancy: 28.4 % / Biso Wilson estimate: 39.9 Å2 / Net I/σ(I): 36.94
Reflection shellResolution: 1.75→37.591 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHENIX(1.13_2998)phasing
PHENIX0.8.6.1refinement
Coot0.8.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.756→37.591 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.2085 1339 4.98 %
Rwork0.1809 --
obs0.1824 26882 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.756→37.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 42 120 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062046
X-RAY DIFFRACTIONf_angle_d0.7842790
X-RAY DIFFRACTIONf_dihedral_angle_d12.823721
X-RAY DIFFRACTIONf_chiral_restr0.055298
X-RAY DIFFRACTIONf_plane_restr0.006351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.756-1.81880.30581160.26362257X-RAY DIFFRACTION87
1.8188-1.89160.29821220.24122349X-RAY DIFFRACTION90
1.8916-1.97770.22611290.19862472X-RAY DIFFRACTION96
1.9777-2.08190.21981340.18482515X-RAY DIFFRACTION97
2.0819-2.21240.21491330.17952563X-RAY DIFFRACTION98
2.2124-2.38320.21491370.17622597X-RAY DIFFRACTION99
2.3832-2.62290.21091380.18172619X-RAY DIFFRACTION100
2.6229-3.00230.23461390.19152658X-RAY DIFFRACTION100
3.0023-3.78210.1781410.17732682X-RAY DIFFRACTION100
3.7821-37.59910.20111500.16882831X-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)
16.2429-0.0985-0.27474.57670.79363.43980.1212-0.33480.36950.6683-0.0553-0.0714-0.28330.0508-0.04320.3797-0.00760.06470.1827-0.00330.21323.670440.795123.2241
26.0962-0.21914.04365.10510.21724.53490.0628-0.14260.12020.8188-0.1194-0.1150.33020.15840.0690.41790.02740.11030.2910.00730.199921.236335.991126.7539
35.74051.72321.34074.303-1.2691.38250.6346-1.28430.36781.2321-0.33530.0063-0.4216-0.1068-0.09150.77520.04160.07640.4547-0.10840.290622.606844.614533.1571
43.8419-4.14070.16066.15230.953.2169-0.2423-1.5284-0.09080.85570.5457-0.05180.08880.099-0.1340.5908-0.03970.09650.39080.04670.312722.742133.023228.6485
53.4256-1.7191-0.16624.097-1.78615.6028-0.0778-0.1168-0.16460.63120.11460.45490.3109-0.268-0.07710.3897-0.01270.09990.148-0.00980.172422.672828.712621.9223
64.4723-0.6024-1.09325.1123-0.36023.5224-0.3030.4282-0.29320.02140.11490.09160.3715-0.2810.16090.2431-0.06070.03690.2016-0.02190.169422.50129.30569.0638
76.0773-0.7921.48856.6247-4.52638.4704-0.0735-0.2594-0.7760.71880.08840.0170.73260.1365-0.02620.54720.01890.06270.1799-0.03260.249926.554718.617321.3415
89.1243-4.25842.49978.5355-0.17339.0652-0.2637-0.06210.56730.31520.1517-1.96530.45521.72180.1830.47280.07130.03190.4964-0.00260.656136.703822.016914.2998
95.3144-1.7428-0.55454.89160.26982.6798-0.07930.3577-0.3834-0.1943-0.11790.24450.3273-0.30070.16920.3008-0.05890.10330.2324-0.0110.169624.263425.72335.8227
105.59411.5204-2.6073.8403-0.81684.5747-0.0040.33860.441-0.19460.1283-0.364-0.43140.1205-0.02650.3412-0.01760.09590.23430.04350.385730.344543.5366.2934
116.7176-2.8681-5.0141.68093.30428.08440.2055-0.15030.41640.11930.1137-0.2211-0.8601-0.2279-0.30760.59050.01690.13550.21080.00660.443123.65352.278619.2434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 170 )
8X-RAY DIFFRACTION8chain 'A' and (resid 171 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 206 )
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 246 )
11X-RAY DIFFRACTION11chain 'A' and (resid 247 through 266 )

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