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- PDB-2am4: Crystal Structure of N-Acetylglucosaminyltransferase I in Complex... -

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Basic information

Entry
Database: PDB / ID: 2am4
TitleCrystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP-2-deoxy-2-fluoro-glucose
ComponentsAlpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / N-Acetylglucosaminyltransferase / glycosyltransferase / UDP-GlcNAc / UDP-2-deoxy-2-fluoro-glucose
Function / homology
Function and homology information


alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine catabolic process / protein N-acetylglucosaminyltransferase activity / mannose metabolic process / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Golgi medial cisterna / manganese ion binding / in utero embryonic development ...alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine catabolic process / protein N-acetylglucosaminyltransferase activity / mannose metabolic process / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Golgi medial cisterna / manganese ion binding / in utero embryonic development / Golgi membrane / perinuclear region of cytoplasm
Similarity search - Function
N-Acetylglucosaminyltransferase I, Domain 2 / : / Glycosyl transferase, family 13 / GNT-I family / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Chem-U2F / Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRini, J.M. / Gordon, R.D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: X-ray Crystal Structures of Rabbit N-acetylglucosaminyltransferase I (GnT I) in Complex with Donor Substrate Analogues.
Authors: Gordon, R.D. / Sivarajah, P. / Satkunarajah, M. / Ma, D. / Tarling, C.A. / Vizitiu, D. / Withers, S.G. / Rini, J.M.
History
DepositionAug 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5335
Polymers39,7251
Non-polymers8074
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.917, 82.501, 102.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / N-glycosyl-oligosaccharide-glycoprotein N- acetylglucosaminyltransferase I / GNT-I / GlcNAc-T I


Mass: 39725.172 Da / Num. of mol.: 1 / Fragment: residues 106-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line: GnT1-5G5 / Gene: MGAT1, GNT1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P27115, alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 40% PEK 6000, 1M Tris, MnCl2, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9363 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2003
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9363 Å / Relative weight: 1
ReflectionResolution: 1.67→51.2 Å / Num. all: 39174 / Num. obs: 37235 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 46 / Limit k min: 0 / Limit l max: 59 / Limit l min: 0 / Observed criterion F max: 370116.78 / Observed criterion F min: 0.32
Reflection shellResolution: 1.7→1.81 Å / % possible all: 84.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO9, 1FOA

1fo9

1foa


Resolution: 1.7→29.8 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3740 10 %RANDOM
Rwork0.193 ---
all-38954 --
obs-37233 95.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 40.6974 Å2 / ksol: 0.396322 e/Å3
Displacement parametersBiso max: 53.76 Å2 / Biso mean: 18.05 Å2 / Biso min: 5.41 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.03 Å
Luzzati d res high-1.7
Refinement stepCycle: LAST / Resolution: 1.7→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 49 268 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg23.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.89
X-RAY DIFFRACTIONx_mcbond_it1.442
X-RAY DIFFRACTIONx_mcangle_it1.993
X-RAY DIFFRACTIONx_scbond_it3.434.5
X-RAY DIFFRACTIONx_scangle_it4.716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.7-1.810.24556110.50.21347840.016371534583.9
1.81-1.950.25163410.40.21254410.016425607594.6
1.95-2.140.2445849.30.21156860.016428627097.5
2.14-2.450.2264610.20.19257000.0096457634698.3
2.45-3.090.2026289.70.17958390.0086523646799.1
3.09-29.80.268710.20.18660430.0086780673099.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_NOHYDROGEN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
X-RAY DIFFRACTION5U2F.PARAMU2F.TOP

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