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- PDB-1nou: Native human lysosomal beta-hexosaminidase isoform B -

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Basic information

Entry
Database: PDB / ID: 1nou
TitleNative human lysosomal beta-hexosaminidase isoform B
Componentsbeta-hexosaminidase beta chain
KeywordsHYDROLASE / (beta/alpha)8-barrel / homodimer / family 20 glycosidase
Function / homology
Function and homology information


beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / penetration of zona pellucida / CS/DS degradation / Hyaluronan uptake and degradation / male courtship behavior / cortical granule ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / penetration of zona pellucida / CS/DS degradation / Hyaluronan uptake and degradation / male courtship behavior / cortical granule / glycosaminoglycan metabolic process / acetylglucosaminyltransferase activity / astrocyte cell migration / beta-N-acetylhexosaminidase activity / hyaluronan catabolic process / phospholipid biosynthetic process / maintenance of location in cell / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / lipid storage / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / azurophil granule / oogenesis / lysosome organization / neuromuscular process controlling balance / single fertilization / myelination / lysosomal lumen / acrosomal vesicle / skeletal system development / locomotory behavior / sensory perception of sound / intracellular calcium ion homeostasis / neuron cellular homeostasis / azurophil granule lumen / regulation of cell shape / lysosome / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / membrane
Similarity search - Function
Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsMark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease
Authors: Mark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 7, 2012Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-hexosaminidase beta chain
B: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5918
Polymers116,3702
Non-polymers1,2216
Water4,071226
1
A: beta-hexosaminidase beta chain
hetero molecules

A: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5878
Polymers116,3702
Non-polymers1,2176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5030 Å2
ΔGint-25 kcal/mol
Surface area37680 Å2
MethodPISA
2
B: beta-hexosaminidase beta chain
hetero molecules

B: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5958
Polymers116,3702
Non-polymers1,2256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area4290 Å2
ΔGint-7 kcal/mol
Surface area37500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.465, 112.465, 397.867
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein beta-hexosaminidase beta chain / N-acetyl-beta-glucosaminidase / Beta-N-acetylhexosaminidase / Hexosaminidase B


Mass: 58184.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P07686, beta-N-acetylhexosaminidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.22 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5 mg/ml HexB [final], 50% saturated ammonium sulphate, and 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Mahuran, D.J., (1980) Can. J. Biochem., 58, 287.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2001 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent cylindrical Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 58844 / Observed criterion σ(I): -3
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 35 Å / % possible obs: 99.5 % / Num. measured all: 2772717 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 99.7 % / Num. unique obs: 2894 / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 4.89

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→34.71 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.799 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.215 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23121 2944 5 %RANDOM
Rwork0.20114 ---
obs0.20266 55895 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.103 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å21.42 Å20 Å2
2--2.84 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7756 0 79 226 8061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218067
X-RAY DIFFRACTIONr_bond_other_d0.0030.027137
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.94510965
X-RAY DIFFRACTIONr_angle_other_deg1.1992.99316609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4013954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.106151389
X-RAY DIFFRACTIONr_chiral_restr0.0960.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021700
X-RAY DIFFRACTIONr_nbd_refined0.1790.31505
X-RAY DIFFRACTIONr_nbd_other0.1370.36798
X-RAY DIFFRACTIONr_nbtor_other0.4510.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5877
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0720.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.524
X-RAY DIFFRACTIONr_mcbond_it0.5271.54798
X-RAY DIFFRACTIONr_mcangle_it1.03627788
X-RAY DIFFRACTIONr_scbond_it1.68633269
X-RAY DIFFRACTIONr_scangle_it2.6694.53177
LS refinement shellResolution: 2.4→2.465 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 208
Rwork0.228 3927
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5123-0.11320.09870.57-0.02051.57170.01590.0070.0260.05870.0610.0685-0.0232-0.1974-0.07680.04950.0314-0.00030.14650.05230.152514.012929.433223.4167
20.44220.0208-0.31360.6206-0.34881.44160.0250.07720.09610.16880.01090.0279-0.20660.0437-0.03590.0981-0.07950.01780.07160.02110.180149.005552.343231.9311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA55 - 5526 - 503
2X-RAY DIFFRACTION2BB55 - 5526 - 503
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.0112
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.59

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