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

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Basic information

Entry
Database: PDB / ID: 2gam
TitleX-ray crystal structure of murine leukocyte-type Core 2 b1,6-N-acetylglucosaminyltransferase (C2GnT-L) in complex with Galb1,3GalNAc
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: 2.7 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: 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
C: beta-1,6-N-acetylglucosaminyltransferase
D: beta-1,6-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,8138
Polymers181,2804
Non-polymers1,5334
Water4,540252
1
A: beta-1,6-N-acetylglucosaminyltransferase
B: beta-1,6-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4074
Polymers90,6402
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: beta-1,6-N-acetylglucosaminyltransferase
D: beta-1,6-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4074
Polymers90,6402
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-5 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.498, 80.585, 102.325
Angle α, β, γ (deg.)73.61, 76.26, 64.56
Int Tables number1
Space group name H-MP1

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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.: 4
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: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 59.8 %
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, 20mM Galb1,3GalNAc, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0729 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 12, 2003
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0729 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 72212 / Num. obs: 69466 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.112 / Χ2: 1.391 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / Num. unique all: 5671 / Rsym value: 0.577 / Χ2: 1.104 / % possible all: 78.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.667 / Packing: 0.48
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.4 0
Translation4 Å15 Ågeneral: ! target for PC-refinement= e2e299.4 0
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.58-200.9480.891081
7.75-9.580.9320.8651091
6.81-7.750.910.8321102
6.21-6.810.9080.8271097
5.77-6.210.9420.8821105
5.44-5.770.9060.8311105
5.17-5.440.9290.8521087
4.95-5.170.9220.8441110
4.76-4.950.9430.8781104
4.6-4.760.9590.9161061
4.46-4.60.9310.8541111
4.33-4.460.940.8831095
4.22-4.330.9280.8581123
4.12-4.220.9080.8241087
4.03-4.120.9170.8411111
3.94-4.030.8960.8061085
3.86-3.940.9030.8131113
3.79-3.860.8970.8191129
3.72-3.790.9210.8471071
3.66-3.720.9030.8311082
3.6-3.660.8830.7951133
3.55-3.60.9040.821105
3.49-3.550.8890.8051074
3.45-3.490.8940.8051118
3.4-3.450.8680.781132
3.36-3.40.8740.7771067
3.31-3.360.8660.7651121
3.27-3.310.8540.7551105
3.24-3.270.8960.8091099
3.2-3.240.8990.8161090
3.16-3.20.8640.7741113
3.13-3.160.8640.7671150
3.1-3.130.8410.7431032
3.07-3.10.8430.7411135
3.04-3.070.8380.7211084
3.01-3.040.8480.741145
2.98-3.010.8020.6881094
2.96-2.980.7970.6841102
2.93-2.960.7850.6611084
2.91-2.930.8530.7571131
2.88-2.910.8460.7441099
2.86-2.880.8160.7161091
2.84-2.860.8360.7251063
2.82-2.840.7810.6631141
2.8-2.820.8280.7261144
2.78-2.80.8090.6991011
2.76-2.780.7640.6551139
2.74-2.760.7690.651091
2.72-2.740.7690.6521056
2.7-2.720.770.6591082

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.502data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GAK

2gak


Resolution: 2.7→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 5592 -random
Rwork0.217 ---
all0.217 55202 --
obs0.217 54982 99.6 %-
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å22.55 Å2-4.47 Å2
2---10.71 Å21.41 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11929 0 104 252 12285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.389 924 -
Rwork0.312 --
obs-8153 98.9 %

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