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- PDB-3lmy: The Crystal Structure of beta-hexosaminidase B in complex with Py... -

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Basic information

Entry
Database: PDB / ID: 3lmy
TitleThe Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine
ComponentsBeta-hexosaminidase subunit beta
KeywordsHYDROLASE / 6-stranded anti-parallel beta-sheet / TIM barrel / Disease mutation / Disulfide bond / Gangliosidosis / Glycoprotein / Glycosidase / Lysosome
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
Chem-CP6 / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 2.8 Å
AuthorsBateman, K.S. / Cherney, M.M. / Withers, S.G. / Mahuran, D.J. / Tropak, M. / James, M.N.G.
CitationJournal: To be Published
Title: The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine
Authors: Bateman, K.S. / Cherney, M.M. / Withers, S.G. / Mahuran, D.J. / Tropak, M. / James, M.N.G.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Beta-hexosaminidase subunit beta
B: Beta-hexosaminidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,07112
Polymers126,3602
Non-polymers2,71010
Water1,40578
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A: Beta-hexosaminidase subunit beta
hetero molecules

A: Beta-hexosaminidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,91510
Polymers126,3602
Non-polymers2,5558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6210 Å2
ΔGint-16 kcal/mol
Surface area38240 Å2
MethodPISA
2
B: Beta-hexosaminidase subunit beta
hetero molecules

B: Beta-hexosaminidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,22614
Polymers126,3602
Non-polymers2,86612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6280 Å2
ΔGint10 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.898, 113.898, 397.427
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-hexosaminidase subunit beta / N-acetyl-beta-glucosaminidase subunit beta / Beta-N-acetylhexosaminidase subunit beta / ...N-acetyl-beta-glucosaminidase subunit beta / Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto-oncogene 7 protein / HCC-7


Mass: 63180.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P07686, beta-N-acetylhexosaminidase

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Sugars , 4 types, 7 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 1
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
#4: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 81 molecules

#6: Chemical ChemComp-CP6 / 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE / PYRIMETHAMINE


Mass: 248.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN4 / Comment: medication, antiparasitic*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50% ammonium sulfate, 50mM potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2008
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→35.9 Å / Num. obs: 35710 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.1 / % possible all: 87.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
CCP4model building
REFMAC5.5.0055refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: Isomorphous replacement
Starting model: PDB entry 1NOU

1nou


Resolution: 2.8→35.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 29.405 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.17 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1801 5 %RANDOM
Rwork0.194 ---
obs0.197 33909 92.2 %-
all-54068 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å21.23 Å20 Å2
2--2.46 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.447 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7750 0 176 78 8004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.97511118
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0515953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02123.602372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.324151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4211546
X-RAY DIFFRACTIONr_chiral_restr0.1150.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216220
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6621.54790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35927781
X-RAY DIFFRACTIONr_scbond_it2.40633375
X-RAY DIFFRACTIONr_scangle_it4.1364.53337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 117 -
Rwork0.335 2272 -
obs--86 %
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)
12.3522-0.6041-0.30931.96390.52111.70330.03060.14580.0905-0.220.055-0.193-0.08660.1635-0.08550.1010.03180.0210.16340.01910.026329.48230.4685.022
20.6949-0.19190.05831.04840.47141.4283-0.0124-0.04450.02240.12940.08540.04750.0263-0.186-0.07290.05970.03990.01440.08840.0320.01529.34629.39529.837
31.25030.32660.09762.9071-1.02552.9160.076-0.25050.07730.43750.08310.1675-0.2686-0.1566-0.15910.2141-0.03180.09650.1302-0.02180.060636.6749.40451.046
40.3435-0.0509-0.1450.6785-0.55171.49040.03290.03610.08130.084-0.0265-0.0444-0.17840.0715-0.00640.0911-0.07840.00370.08690.00930.020854.73754.04525.042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 198
2X-RAY DIFFRACTION2A199 - 552
3X-RAY DIFFRACTION3B54 - 198
4X-RAY DIFFRACTION4B199 - 552

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