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- PDB-1jv3: CRYSTAL STRUCTURE OF HUMAN AGX1 COMPLEXED WITH UDPGALNAC -

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Basic information

Entry
Database: PDB / ID: 1jv3
TitleCRYSTAL STRUCTURE OF HUMAN AGX1 COMPLEXED WITH UDPGALNAC
ComponentsGlcNAc1P uridyltransferase isoform 1: AGX1
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / ALTERNATIVE SPLICING
Function / homology
Function and homology information


protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production / antiviral innate immune response ...protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / positive regulation of type I interferon production / antiviral innate immune response / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #100 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Seminal Fluid Protein PDC-109 (Domain B) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Ribbon / Alpha-Beta Complex ...Seminal Fluid Protein PDC-109 (Domain B) - #100 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Seminal Fluid Protein PDC-109 (Domain B) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / UDP-N-acetylhexosamine pyrophosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 2.2 Å
AuthorsPeneff, C. / Bourne, Y.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture.
Authors: Peneff, C. / Ferrari, P. / Charrier, V. / Taburet, Y. / Monnier, C. / Zamboni, V. / Winter, J. / Harnois, M. / Fassy, F. / Bourne, Y.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GlcNAc1P uridyltransferase isoform 1: AGX1
B: GlcNAc1P uridyltransferase isoform 1: AGX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4074
Polymers114,1922
Non-polymers1,2152
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-22 kcal/mol
Surface area40050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.735, 70.769, 95.384
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GlcNAc1P uridyltransferase isoform 1: AGX1 / UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE


Mass: 57095.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UAP1 / Plasmid: pRU277 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1blue
References: UniProt: Q16222, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: peg600, Imidazole/malate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.000001 mMprotein1drop
2100 mMTris-HCl1drop
320 mM1dropKCl
45 mM1dropMgCl2
534 %PEG6001reservoir
60.2 Mimidazole/malate1reservoirpH5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2001
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 66084 / Num. obs: 64858 / % possible obs: 97.62 % / Observed criterion σ(I): 1.8 / Redundancy: 2.62 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.4823
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.52 % / Mean I/σ(I) obs: 1.84 / Num. unique all: 5529 / Rsym value: 0.37 / % possible all: 98.18
Reflection
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: rigid body
Starting model: pdb code: 1JV1

1jv1


Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1930205.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1684 3 %RANDOM
Rwork0.19 ---
all-57944 --
obs-56389 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1159 Å2 / ksol: 0.366139 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.15 Å20 Å2-4.73 Å2
2---6.14 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 78 615 8477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 278 3 %
Rwork0.232 9111 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2UD1-GAL.PARAMUD1.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.232

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