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- PDB-1omx: Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransfera... -

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Basic information

Entry
Database: PDB / ID: 1omx
TitleCrystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2)
ComponentsAlpha-1,4-N-acetylhexosaminyltransferase EXTL2
KeywordsTRANSFERASE / DXD motif / Rossmann fold
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 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 26, 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 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)66,9795
Polymers66,7932
Non-polymers1863
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-7 kcal/mol
Surface area20810 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)267,91520
Polymers267,1708
Non-polymers74512
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 area29540 Å2
ΔGint-132 kcal/mol
Surface area67660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.903, 125.903, 83.068
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-12% PEG3000, 200mM MgCl2, 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 5, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 26171 / Num. obs: 26171 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 127306 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 86.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→23.3 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1230 4.8 %RANDOM
Rwork0.203 ---
all0.205 26848 --
obs0.203 25618 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3109 Å2 / ksol: 0.332343 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å20 Å2
2--2.17 Å20 Å2
3----4.34 Å2
Refine analyzeLuzzati coordinate error free: 0.34 Å / Luzzati sigma a free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 12 182 4134
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_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 185 5 %
Rwork0.267 3493 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EDO.PAREDO.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Highest resolution: 2.4 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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