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- PDB-1kws: CRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1kws
TitleCRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX WITH THE ACTIVE UDP-GLCUA DONOR
ComponentsBETA-1,3-GLUCURONYLTRANSFERASE 3
KeywordsTRANSFERASE / DXD / NTP binding domain
Function / homology
Function and homology information


dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / positive regulation of catalytic activity ...dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / positive regulation of catalytic activity / positive regulation of intracellular protein transport / cis-Golgi network / : / protein phosphatase activator activity / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / 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
: / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsPedersen, L.C. / Darden, T.A. / Negishi, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA.
Authors: Pedersen, L.C. / Darden, T.A. / Negishi, M.
History
DepositionJan 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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_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 / _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: BETA-1,3-GLUCURONYLTRANSFERASE 3
B: BETA-1,3-GLUCURONYLTRANSFERASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2556
Polymers57,9842
Non-polymers1,2704
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-51 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.625, 47.978, 102.152
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-1,3-GLUCURONYLTRANSFERASE 3 / glucuronosyltransferase I


Mass: 28992.064 Da / Num. of mol.: 2 / Fragment: Residue 76-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O94766
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, MME-PEG2K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlGlcAT-I1drop
225 mMHEPES1droppH7.5
350 mM1dropNaCl
410 mM1dropMnCl2
510 mMUDP-GlcUA1drop
621 %PEG2000 MME1reservoir
7100 mMMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 9, 2000 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 32779 / Num. obs: 32764 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3 / Num. unique all: 3134 / % possible all: 96
Reflection
*PLUS
Num. obs: 32779 / Num. measured all: 112504 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.309

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1FGG

1fgg


Resolution: 2.1→24.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 139032.36 / 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
Rfree0.223 1603 5 %RANDOM
Rwork0.187 ---
obs0.188 32189 97.6 %-
all-32779 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4552 Å2 / ksol: 0.351798 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.07 Å20 Å20.93 Å2
2---2.04 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 76 359 4254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 266 5.2 %
Rwork0.22 4826 -
obs-4826 93.5 %
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 DIFFRACTION4GLC.PARAMGLC.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.188 / Rfactor obs: 0.187 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22

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