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- PDB-5bro: Crystal structure of modified HexB (modB) -

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Basic information

Entry
Database: PDB / ID: 5bro
TitleCrystal structure of modified HexB (modB)
ComponentsBeta-hexosaminidase subunit betaHexosaminidase
KeywordsHYDROLASE / Therapeutic enzyme
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 / glycosaminoglycan metabolic process / CS/DS degradation / Hyaluronan uptake and degradation / penetration of zona pellucida / maintenance of location in cell ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / glycosaminoglycan metabolic process / CS/DS degradation / Hyaluronan uptake and degradation / penetration of zona pellucida / maintenance of location in cell / male courtship behavior / ganglioside catabolic process / cortical granule / acetylglucosaminyltransferase activity / astrocyte cell migration / oligosaccharide catabolic process / hyaluronan catabolic process / phospholipid biosynthetic process / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / lipid storage / Glycosphingolipid catabolism / azurophil granule / oogenesis / lysosome organization / single fertilization / neuromuscular process controlling balance / myelination / lysosomal lumen / acrosomal vesicle / locomotory behavior / skeletal system development / 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 / membrane / identical protein binding
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
FORMIC ACID / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKitakaze, K. / Maita, N. / Itoh, K.
Citation
Journal: J.Clin.Invest. / Year: 2016
Title: Protease-resistant modified human beta-hexosaminidase B ameliorates symptoms in GM2 gangliosidosis model.
Authors: Kitakaze, K. / Mizutani, Y. / Sugiyama, E. / Tasaki, C. / Tsuji, D. / Maita, N. / Hirokawa, T. / Asanuma, D. / Kamiya, M. / Sato, K. / Setou, M. / Urano, Y. / Togawa, T. / Otaka, A. / Sakuraba, H. / Itoh, K.
#1: Journal: Mol. Ther. / Year: 2011
Title: Therapeutic potential of intracerebroventricular replacement of modified human beta-hexosaminidase B for GM2 gangliosidosis.
Authors: Matsuoka, K. / Tamura, T. / Tsuji, D. / Dohzono, Y. / Kitakaze, K. / Ohno, K. / Saito, S. / Sakuraba, H. / Itoh, K.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7265
Polymers58,7391
Non-polymers9874
Water2,702150
1
A: Beta-hexosaminidase subunit beta
hetero molecules

A: Beta-hexosaminidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,45310
Polymers117,4792
Non-polymers1,9748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area5780 Å2
ΔGint7 kcal/mol
Surface area38740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.470, 126.470, 88.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

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


Mass: 58739.438 Da / Num. of mol.: 1 / Mutation: R312G, Q313S, N314E, K315P, D452N, L453R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEXB, HCC7 / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M Sodium Formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 28619 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementResolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.289 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24014 1428 5 %RANDOM
Rwork0.18749 ---
obs0.19009 27149 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.347 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---1.04 Å2-0 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 65 150 4167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194136
X-RAY DIFFRACTIONr_bond_other_d0.0010.023829
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9655624
X-RAY DIFFRACTIONr_angle_other_deg0.77138810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1665488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78623.579190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7561524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02979
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_it3.83.3751957
X-RAY DIFFRACTIONr_mcbond_other3.7993.3751958
X-RAY DIFFRACTIONr_mcangle_it5.4515.0542444
X-RAY DIFFRACTIONr_mcangle_other5.455.0552445
X-RAY DIFFRACTIONr_scbond_it4.8713.8352177
X-RAY DIFFRACTIONr_scbond_other4.8713.8342175
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1795.5723179
X-RAY DIFFRACTIONr_long_range_B_refined8.68427.3744851
X-RAY DIFFRACTIONr_long_range_B_other8.69227.3744818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 110 -
Rwork0.293 1959 -
obs--99.66 %

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