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- PDB-1bhg: HUMAN BETA-GLUCURONIDASE AT 2.6 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1bhg
TitleHUMAN BETA-GLUCURONIDASE AT 2.6 A RESOLUTION
ComponentsBETA-GLUCURONIDASE
KeywordsGLYCOSIDASE / LYSOSOMAL ENZYME / ACID HYDROLASE
Function / homology
Function and homology information


MPS VII - Sly syndrome (Hyaluronan metabolism) / chondroitin sulfate proteoglycan catabolic process / glycosaminoglycan catabolic process / Hyaluronan degradation / beta-glucuronidase / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / hyaluronan catabolic process / lysosomal lumen ...MPS VII - Sly syndrome (Hyaluronan metabolism) / chondroitin sulfate proteoglycan catabolic process / glycosaminoglycan catabolic process / Hyaluronan degradation / beta-glucuronidase / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / hyaluronan catabolic process / lysosomal lumen / azurophil granule lumen / carbohydrate binding / carbohydrate metabolic process / ficolin-1-rich granule lumen / signaling receptor binding / protein domain specific binding / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.53 Å
AuthorsJain, S. / Drendel, W.B.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs.
Authors: Jain, S. / Drendel, W.B. / Chen, Z.W. / Mathews, F.S. / Sly, W.S. / Grubb, J.H.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary Crystallographic Studies of Human Beta-Glucuronidase
Authors: Drendel, W.B. / Grubb, J.H. / Sly, W.S. / Chen, Z. / Mathews, F.S. / Jain, S.
History
DepositionMar 4, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-GLUCURONIDASE
B: BETA-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6454
Polymers141,5262
Non-polymers3,1192
Water00
1
A: BETA-GLUCURONIDASE
B: BETA-GLUCURONIDASE
hetero molecules

A: BETA-GLUCURONIDASE
B: BETA-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,2898
Polymers283,0514
Non-polymers6,2384
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area28040 Å2
ΔGint32 kcal/mol
Surface area85150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.100, 124.400, 134.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BETA-GLUCURONIDASE / GUS GENE PRODUCT


Mass: 70762.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LYSOSOMAL ENZYME / Source: (gene. exp.) Homo sapiens (human) / Cell line: MOUSE L-CELL LINE / Gene: HUMAN PLACENTAL GUS GENE CDNA / Organ: PLACENTA / Organelle: LYSOSOME / Plasmid: PMSXND / Gene (production host): HUMAN PLACENTAL GUS GENE CDNA / Production host: Mus musculus (house mouse) / References: UniProt: P08236, beta-glucuronidase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 49.4 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.1 mg/mlprotein1drop
215 %MPD1drop
35 mMTris-HCl1drop
40.01 %(w/v)sodium azide1drop
530 %MPD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 10, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 46839 / % possible obs: 93.23 % / Observed criterion σ(I): 1 / Redundancy: 4.71 % / Rmerge(I) obs: 0.0779
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
X-PLORrefinement
XENGEN(ANDERSONdata reduction
HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
RefinementResolution: 2.53→7 Å / σ(F): 2
RfactorNum. reflection
Rfree0.31 -
Rwork0.231 -
obs0.231 44237
Refinement stepCycle: LAST / Resolution: 2.53→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 210 0 10190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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