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- PDB-1on6: Crystal structure of mouse alpha-1,4-N-acetylhexosaminotransferas... -

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Basic information

Entry
Database: PDB / ID: 1on6
TitleCrystal structure of mouse alpha-1,4-N-acetylhexosaminotransferase (EXTL2) in complex with UDPGlcNAc
ComponentsAlpha-1,4-N-acetylhexosaminyltransferase EXTL2
KeywordsTRANSFERASE / Rossmann fold / DXD motif
Function / homology
Function and homology information


UDP-N-acetylgalactosamine metabolic process / alpha-1,4-N-acetylgalactosaminyltransferase activity / glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity / glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosamine metabolic process / glycosaminoglycan binding / manganese ion binding / endoplasmic reticulum membrane / nucleoplasm / cytosol
Similarity search - Function
Glycosyl transferase 64 domain / Glycosyl transferase family 64 domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Exostosin-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPedersen, L.C. / Dong, J. / Taniguchi, F. / Kitagawa, H. / Krahn, J.M. / Pedersen, L.G. / Sugahara, K. / Negishi, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of an alpha-1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis
Authors: Pedersen, L.C. / Dong, J. / Taniguchi, F. / Kitagawa, H. / Krahn, J.M. / Pedersen, L.G. / Sugahara, K. / Negishi, M.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS NOT KNOWN.
Remark 999SEQUENCE Although the catalytic domain containing residues 38-330 were cloned into the expression ...SEQUENCE Although the catalytic domain containing residues 38-330 were cloned into the expression system, the exact N-termini of the final product is not known due to cleavage of the fusion protein with a non-specific protease. However there is electron density starting at residue 62.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2418
Polymers66,7932
Non-polymers1,4496
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-39 kcal/mol
Surface area20940 Å2
MethodPISA
2
A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,96532
Polymers267,1708
Non-polymers5,79524
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area38440 Å2
ΔGint-278 kcal/mol
Surface area66980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.064, 126.064, 83.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 / Alpha-GalNAcT EXTL2 / EXT-related protein 2 / Exostosin-like 2


Mass: 33396.312 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: EXTL2 OR EXTR2 / Plasmid: pMal-2c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9ES89, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3000, mgcl2, cacodyltate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMHEPES1droppH7.5
2100 mM1dropNaCl
30.1 Msodium cacodylate1reservoirpH7.5
410-12 %PEG30001reservoir
5200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 26, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 27856 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 23.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2184 / Rsym value: 0.299 / % possible all: 72.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 248026 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 72.9 % / Rmerge(I) obs: 0.299

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo enzyme pdb:1OMX

1omx


Resolution: 2.3→19.93 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1344 4.9 %RANDOM
Rwork0.196 ---
all0.198 28944 --
obs0.196 27600 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0568 Å2 / ksol: 0.349753 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.51 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 88 202 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 173 4.9 %
Rwork0.234 3389 -
obs--71.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3UD1.PARUD1.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5EDO.PAREDO.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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