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- PDB-1foa: CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINYLTRANSFERASE I -

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Basic information

Entry
Database: PDB / ID: 1foa
TitleCRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINYLTRANSFERASE I
ComponentsALPHA-1,3-MANNOSYL-GLYCOPROTEIN BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE
KeywordsTRANSFERASE / Donor substrate and metal ion complex / ALPHA-1 / 3-MANNOSYL-GLYCOPROTEIN / BETA-1 / 2-N-ACETYLGLUCOSAMINYLTRANSFERASE / N-ACETYLGLUCOSAMINYLTRANSFERASE I
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 / protein N-linked glycosylation via asparagine / mannose metabolic process / 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 / protein N-linked glycosylation via asparagine / mannose metabolic process / 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-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsUnligil, U.M. / Zhou, S. / Yuwaraj, S. / Sarkar, M. / Schachter, H. / Rini, J.M.
CitationJournal: EMBO J. / Year: 2000
Title: X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
Authors: Unligil, U.M. / Zhou, S. / Yuwaraj, S. / Sarkar, M. / Schachter, H. / Rini, J.M.
History
DepositionAug 26, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-1,3-MANNOSYL-GLYCOPROTEIN BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2995
Polymers40,4531
Non-polymers8464
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.541, 82.190, 101.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein ALPHA-1,3-MANNOSYL-GLYCOPROTEIN BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE


Mass: 40452.996 Da / Num. of mol.: 1 / Fragment: RESIDUES 100-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: MODIFIED PVT-BAC-HIS / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
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-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#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.: 275 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 8000, potassium chloride, glycerol, Tris, MES, UDP-GlcNAc, manganese chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMMES1drop
3270 mM1dropKCl
42 mM1dropMnCl2
510 mMUDP-GlcNAc1drop
615-25 %PEG80001reservoir
7100 mMTris-HCl1reservoir
80-5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.0713
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0713 Å / Relative weight: 1
ReflectionResolution: 1.8→34.25 Å / Num. all: 64537 / Num. obs: 42919 / % possible obs: 70.3 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.017 / Num. unique all: 4803 / % possible all: 47.2
Reflection
*PLUS
Num. measured all: 64537

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementResolution: 1.8→34.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2424931.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2176 5.1 %RANDOM
Rwork0.185 ---
obs0.185 42919 70.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.84 Å2 / ksol: 0.4085 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.28 Å20 Å20 Å2
2---1.15 Å20 Å2
3---5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 52 275 3138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 179 3.7 %
Rwork0.281 4623 -
obs--47.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3UDPGLCNAC.PARAMUDPGLCNAC.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.316 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.281

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