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- PDB-8og1: Exostosin-like 3 apo enzyme -

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Basic information

Entry
Database: PDB / ID: 8og1
TitleExostosin-like 3 apo enzyme
ComponentsExostosin-like 3
KeywordsTRANSFERASE / Glycosyltransferase / heparan sulfate
Function / homology
Function and homology information


glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / positive regulation of detection of glucose / protein-hormone receptor activity / positive regulation of keratinocyte proliferation / heparan sulfate proteoglycan biosynthetic process / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / XBP1(S) activates chaperone genes / protein glycosylation ...glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / positive regulation of detection of glucose / protein-hormone receptor activity / positive regulation of keratinocyte proliferation / heparan sulfate proteoglycan biosynthetic process / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / XBP1(S) activates chaperone genes / protein glycosylation / glycosyltransferase activity / negative regulation of cytokine production involved in inflammatory response / negative regulation of inflammatory response / positive regulation of cell growth / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / nucleus / plasma membrane
Similarity search - Function
Exostosin-like / Exostosin, GT47 domain / Exostosin GT47 domain / Glycosyl transferase 64 domain / Glycosyl transferase family 64 domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSammon, D. / Hohenester, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T01279X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of decision-making in glycosaminoglycan biosynthesis.
Authors: Sammon, D. / Krueger, A. / Busse-Wicher, M. / Morgan, R.M. / Haslam, S.M. / Schumann, B. / Briggs, D.C. / Hohenester, E.
History
DepositionMar 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exostosin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3143
Polymers101,6131
Non-polymers1,7012
Water5,891327
1
A: Exostosin-like 3
hetero molecules

A: Exostosin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,6276
Polymers203,2262
Non-polymers3,4014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area15280 Å2
ΔGint-5 kcal/mol
Surface area53490 Å2
Unit cell
Length a, b, c (Å)120.900, 120.900, 127.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Exostosin-like 3 / EXT-related protein 1 / Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase ...EXT-related protein 1 / Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / Hereditary multiple exostoses gene isolog / Multiple exostosis-like protein 3 / Putative tumor suppressor protein EXTL3


Mass: 101613.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXTL3, EXTL1L, EXTR1, KIAA0519 / Production host: Homo sapiens (human)
References: UniProt: O43909, glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 12.5% (w/v) PEG3350, 0.1 M sodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.58→34.9 Å / Num. obs: 146847 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 26.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.6
Reflection shellResolution: 1.58→1.62 Å / Rmerge(I) obs: 1.889 / Num. unique obs: 10580 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3769refinement
PHENIX1.18rc1_3769refinement
xia23.dev.661-g1a4ae04e6data reduction
xia23.dev.661-g1a4ae04e6data scaling
PHENIX1.18rc1_3769phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→34.76 Å / SU ML: 0.1949 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 7422 5.06 %
Rwork0.184 139347 -
obs0.1853 146769 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.17 Å2
Refinement stepCycle: LAST / Resolution: 1.58→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 114 327 6163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01036034
X-RAY DIFFRACTIONf_angle_d1.10438228
X-RAY DIFFRACTIONf_chiral_restr0.0605929
X-RAY DIFFRACTIONf_plane_restr0.00831049
X-RAY DIFFRACTIONf_dihedral_angle_d21.50292247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.35322520.34984498X-RAY DIFFRACTION97.48
1.6-1.620.39752320.33754574X-RAY DIFFRACTION99.03
1.62-1.640.32792470.31454604X-RAY DIFFRACTION99.98
1.64-1.660.32272580.29084620X-RAY DIFFRACTION99.98
1.66-1.680.31472830.28724570X-RAY DIFFRACTION100
1.68-1.70.29482280.27954620X-RAY DIFFRACTION100
1.7-1.730.32732640.26874613X-RAY DIFFRACTION100
1.73-1.750.27292330.25274622X-RAY DIFFRACTION100
1.75-1.780.25732400.23934614X-RAY DIFFRACTION99.98
1.78-1.810.27832200.23484637X-RAY DIFFRACTION100
1.81-1.840.23522500.22144601X-RAY DIFFRACTION100
1.84-1.870.23482470.20924612X-RAY DIFFRACTION100
1.87-1.910.22722080.20764675X-RAY DIFFRACTION100
1.91-1.950.21532400.20474630X-RAY DIFFRACTION100
1.95-1.990.23012910.20364599X-RAY DIFFRACTION100
1.99-2.040.22852450.19924618X-RAY DIFFRACTION100
2.04-2.090.24742410.19944668X-RAY DIFFRACTION100
2.09-2.140.20322430.19444611X-RAY DIFFRACTION99.98
2.14-2.210.22792340.19224655X-RAY DIFFRACTION100
2.21-2.280.21142710.18654636X-RAY DIFFRACTION100
2.28-2.360.22812270.18664652X-RAY DIFFRACTION100
2.36-2.450.20522640.1834613X-RAY DIFFRACTION100
2.45-2.570.19872050.17464725X-RAY DIFFRACTION100
2.57-2.70.22132530.18884656X-RAY DIFFRACTION100
2.7-2.870.19642510.18534682X-RAY DIFFRACTION100
2.87-3.090.21992460.19114684X-RAY DIFFRACTION100
3.09-3.40.2222600.18284683X-RAY DIFFRACTION100
3.4-3.890.2062340.15894755X-RAY DIFFRACTION100
3.9-4.90.17232720.13854728X-RAY DIFFRACTION99.98
4.91-34.760.17512830.16874892X-RAY DIFFRACTION99.83

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