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- PDB-1fgg: CRYSTAL STRUCTURE OF 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1fgg
TitleCRYSTAL STRUCTURE OF 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) COMPLEXED WITH GAL-GAL-XYL, UDP, AND MN2+
ComponentsGLUCURONYLTRANSFERASE I
KeywordsTRANSFERASE / glucuronyltransferase / UDP / DDD
Function / homology
Function and homology information


dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / positive regulation of intracellular protein transport ...dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / positive regulation of intracellular protein transport / cis-Golgi network / positive regulation of catalytic activity / protein phosphatase activator activity / protein glycosylation / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / membrane / metal ion binding
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
: / URIDINE-5'-DIPHOSPHATE / Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPedersen, L.C. / Tsuchida, K. / Kitagawa, H. / Sugahara, K. / Darden, T.A.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Heparan/chondroitin sulfate biosynthesis. Structure and mechanism of human glucuronyltransferase I.
Authors: Pedersen, L.C. / Tsuchida, K. / Kitagawa, H. / Sugahara, K. / Darden, T.A. / Negishi, M.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_src_syn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCURONYLTRANSFERASE I
B: GLUCURONYLTRANSFERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2459
Polymers57,9842
Non-polymers1,2607
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-42 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.842, 48.219, 102.204
Angle α, β, γ (deg.)90.00, 92.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein GLUCURONYLTRANSFERASE I


Mass: 28992.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: O94766
#2: Polysaccharide beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 227 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: monomethyl ether PEG2000, MnCl2, MgCl2, UDP-GlcA, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 23K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
121 %PEG2000 MME1reservoir
20.1 MMES1reservoir
315 mg/mlprotein1drop
425 mMHEPES1drop
550 mM1dropNaOH
65 mM1dropMnCl2
75 mM1dropMgCl2
810 mMUDP-GlcUA1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 69398 / Num. obs: 69398 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.243 / Num. unique all: 2057 / % possible all: 82.5
Reflection
*PLUS
Num. obs: 24398 / Num. measured all: 69398
Reflection shell
*PLUS
% possible obs: 82.5 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→24.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 297269.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1162 4.8 %RANDOM
Rwork0.188 ---
all0.189 24666 --
obs0.189 23982 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.67 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å20 Å20.11 Å2
2---4.56 Å20 Å2
3----0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 77 221 4135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 164 4.8 %
Rwork0.235 3280 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4UDP2.PARUDP2.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.235

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