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- PDB-2gak: X-ray crystal structure of murine leukocyte-type Core 2 b1,6-N-ac... -

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Basic information

Entry
Database: PDB / ID: 2gak
TitleX-ray crystal structure of murine leukocyte-type Core 2 b1,6-N-acetylglucosaminyltransferase (C2GnT-L)
Componentsbeta-1,6-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / glycoprotein / cis-peptide / dimer
Function / homology
Function and homology information


beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity / O-glycan processing, core 2 / O-linked glycosylation of mucins / tissue morphogenesis / kidney morphogenesis / glycoprotein biosynthetic process / Golgi cisterna / positive regulation of leukocyte tethering or rolling / leukocyte tethering or rolling ...beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity / O-glycan processing, core 2 / O-linked glycosylation of mucins / tissue morphogenesis / kidney morphogenesis / glycoprotein biosynthetic process / Golgi cisterna / positive regulation of leukocyte tethering or rolling / leukocyte tethering or rolling / cell adhesion molecule production / response to insulin / trans-Golgi network / Golgi membrane / nucleotide binding / extracellular space
Similarity search - Function
Glycosyl transferase, family 14 / Core-2/I-Branching enzyme
Similarity search - Domain/homology
Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPak, J.E. / Rini, J.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: X-ray Crystal Structure of Leukocyte Type Core 2 beta1,6-N-Acetylglucosaminyltransferase: Evidence for a covergence of metal ion independent glycosyltransferase mechanism.
Authors: Pak, J.E. / Arnoux, P. / Zhou, S. / Sivarajah, P. / Satkunarajah, M. / Xing, X. / Rini, J.M.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: beta-1,6-N-acetylglucosaminyltransferase
B: beta-1,6-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0824
Polymers90,6402
Non-polymers4422
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-5 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.779, 79.979, 104.971
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-665-

HOH

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Components

#1: Protein beta-1,6-N-acetylglucosaminyltransferase / Beta-1 / 3-galactosyl-O-glycosyl-glycoprotein / Core 2 branching enzyme / Core2-GlcNAc-transferase / C2GNT


Mass: 45319.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gcnt1 / Plasmid: pProtA / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q09324, beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG 4000, 0.1M glycine pH=9.0, 0.6M lithium chloride, 3.3% 1,2,3 heptanetriol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 67652 / Num. obs: 67648 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.079 / Χ2: 1.456 / Net I/σ(I): 19.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 8.61 / Num. unique all: 6642 / Rsym value: 0.17 / Χ2: 1.302 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.668 / Packing: 0.486
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.1 0
Translation4 Å15 Ågeneral: ! target for PC-refinement= e2e299.1 0
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.25-20192.7330.9621345
5.8-7.25188.6950.9311377
5.08-5.8189.7340.9451364
4.62-5.08187.1290.9571370
4.3-4.62198.5070.9581373
4.04-4.3194.730.9591352
3.84-4.04184.0650.9611348
3.68-3.84199.9590.9391344
3.54-3.68198.2260.9451340
3.42-3.54165.2850.9511347
3.31-3.42172.9330.9291375
3.21-3.31148.8130.9441345
3.13-3.21153.940.9291337
3.05-3.13143.1550.9251382
2.99-3.05135.5850.9291341
2.92-2.99117.3860.9331358
2.86-2.92106.6340.9541328
2.81-2.86117.5860.9251354
2.76-2.81119.3910.9041322
2.71-2.76103.9380.9411371
2.67-2.7198.5070.9241317
2.63-2.6799.3560.921387
2.59-2.6394.5180.9221321
2.55-2.5990.780.9211356
2.52-2.5592.4630.9141351
2.49-2.5288.3370.931330
2.46-2.4979.9050.9291369
2.43-2.4686.9420.9191327
2.4-2.4393.0690.9091354
2.37-2.477.5570.9251356
2.35-2.3777.7090.9211302
2.32-2.3578.1860.9231406
2.3-2.3279.9850.9241323
2.27-2.376.7660.9051337
2.25-2.2777.4750.9151375
2.23-2.2571.4550.9331322
2.21-2.2370.5360.921338
2.19-2.2162.1650.9271341
2.17-2.1971.2960.8971375
2.15-2.1762.8840.9251295
2.14-2.1560.5560.9311386
2.12-2.1462.9460.9221326
2.1-2.1263.7960.911355
2.09-2.165.5480.8981324
2.07-2.0964.130.8961350
2.06-2.0762.7610.8911339
2.04-2.0661.010.9081340
2.03-2.0457.7670.9151337
2.01-2.0356.2250.8981353
2-2.0158.8460.8961321

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.502data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: selenomethioninyl C2GnT-L

Resolution: 2→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6825 -random
Rwork0.197 ---
all0.197 67528 --
obs0.197 67387 99.8 %-
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å21.08 Å2-5.22 Å2
2--0 Å20.28 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 28 498 6541
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.261 1112 -
Rwork0.213 --
obs-10084 99.9 %

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