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- PDB-1jvd: CRYSTAL STRUCTURE OF HUMAN AGX2 COMPLEXED WITH UDPGLCNAC -

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Basic information

Entry
Database: PDB / ID: 1jvd
TitleCRYSTAL STRUCTURE OF HUMAN AGX2 COMPLEXED WITH UDPGLCNAC
ComponentsUDPGLCNAC PYROPHOSPHORYLASE (AGX2)
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 / antiviral innate immune response / positive regulation of type I interferon production ...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 / antiviral innate immune response / positive regulation of type I interferon production / 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-ACETYLGLUCOSAMINE / UDP-N-acetylhexosamine pyrophosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 29, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: UDPGLCNAC PYROPHOSPHORYLASE (AGX2)
B: UDPGLCNAC PYROPHOSPHORYLASE (AGX2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8924
Polymers117,6782
Non-polymers1,2152
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-21 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.543, 71.281, 91.390
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDPGLCNAC PYROPHOSPHORYLASE (AGX2) / UDP-N-acetylglucosamine pyrophosphorylase


Mass: 58838.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGX2 / Plasmid: pRU277 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1 BLUE
References: UniProt: Q16222, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG600, 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: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 43625 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.062 / Net I/σ(I): 6.2
Reflection
*PLUS
Lowest resolution: 40 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1498298.17 / 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
Rfree0.251 2180 5 %RANDOM
Rwork0.193 ---
obs-43565 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6024 Å2 / ksol: 0.353303 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-15.09 Å20 Å2-4.64 Å2
2---6.1 Å20 Å2
3----8.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 78 310 8055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 333 4.6 %
Rwork0.242 6888 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3UD1.PARAMUD1.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / Rfactor Rwork: 0.242

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