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- PDB-2am5: Crystal Structure of N-Acetylglucosaminyltransferase I in Complex... -

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Basic information

Entry
Database: PDB / ID: 2am5
TitleCrystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP
ComponentsAlpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / N-Acetylglucosaminyltransferase / glycosyltransferase / UDP-GlcNAc / UDP
Function / homology
Function and homology information


alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / : / 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 / : / 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
: / URIDINE-5'-DIPHOSPHATE / Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)40,6458
Polymers39,7251
Non-polymers9207
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.619, 82.029, 101.852
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 / 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
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: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 11, 2003
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→31.94 Å / Num. all: 45466 / Num. obs: 44852 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 311496.49 / Observed criterion F min: 0.32
Reflection shellResolution: 1.6→1.7 Å / % possible all: 94

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO9, 1FOA

1fo9

1foa


Resolution: 1.6→31.94 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
Rfree0.198 2256 5 %RANDOM
Rwork0.177 ---
all-45766 --
obs-44852 98 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 39.1505 Å2 / ksol: 0.416299 e/Å3
Displacement parametersBiso max: 44.79 Å2 / Biso mean: 13.28 Å2 / Biso min: 2.74 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å-0.01 Å
Luzzati d res high-1.6
Refinement stepCycle: LAST / Resolution: 1.6→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 56 261 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_deg24
X-RAY DIFFRACTIONx_torsion_impr_deg0.91
X-RAY DIFFRACTIONx_mcbond_it1.362
X-RAY DIFFRACTIONx_mcangle_it1.983
X-RAY DIFFRACTIONx_scbond_it3.074.5
X-RAY DIFFRACTIONx_scangle_it4.136
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 (%)
1.6-1.70.1923625.10.17467290.017538709194.1
1.7-1.830.2136550.17869920.0117551735797.4
1.83-2.020.2137450.18570640.0117535743898.7
2.02-2.310.2133975.30.17771400.0117583753799.4
2.31-2.910.1883754.90.17272500.017680762599.3
2.91-31.940.1883834.90.17774210.017927780498.4
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 DIFFRACTION5DONOR.PARAMDONOR.TOP

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