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- PDB-1v82: Crystal structure of human GlcAT-P apo form -

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Basic information

Entry
Database: PDB / ID: 1v82
TitleCrystal structure of human GlcAT-P apo form
ComponentsGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
KeywordsTRANSFERASE / glycoprotein / glycocyltransferase / HNK-1 epitope
Function / homology
Function and homology information


galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / chondroitin sulfate proteoglycan biosynthetic process / : / visual learning / carbohydrate metabolic process / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane ...galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / Glycosaminoglycan-protein linkage region biosynthesis / chondroitin sulfate proteoglycan biosynthetic process / : / visual learning / carbohydrate metabolic process / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / extracellular region / metal ion binding / membrane
Similarity search - Function
Glycosyl transferase, family 43 / Glycosyltransferase family 43 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKakuda, S. / Shiba, T. / Ishiguro, M. / Tagawa, H. / Oka, S. / Kajihara, Y. / Kawasaki, T. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1
Authors: Kakuda, S. / Shiba, T. / Ishiguro, M. / Tagawa, H. / Oka, S. / Kajihara, Y. / Kawasaki, T. / Wakatsuki, S. / Kato, R.
History
DepositionDec 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
B: Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2273
Polymers58,0772
Non-polymers1501
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-25 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.111, 85.969, 122.425
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 Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 / Beta-1 / 3-glucuronyltransferase 1 / Glucuronosyltransferase-P / GlcAT-P / UDP-GlcUA:glycoprotein ...Beta-1 / 3-glucuronyltransferase 1 / Glucuronosyltransferase-P / GlcAT-P / UDP-GlcUA:glycoprotein beta- 1 / 3-glucuronyltransferase


Mass: 29038.408 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9P2W7, galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.69 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG5000MME, di-sodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 54710 / Num. obs: 54639 / % possible obs: 96.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.5 / % possible all: 79.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FGG

1fgg


Resolution: 1.85→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2729 -RANDOM
Rwork0.1978 ---
all0.19931 54710 --
obs0.19931 54639 96.3 %-
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 10 381 4343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005211
X-RAY DIFFRACTIONc_angle_deg1.22054

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