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- PDB-1c7s: BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACET... -

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Basic information

Entry
Database: PDB / ID: 1c7s
TitleBETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)
ComponentsBETA-N-ACETYLHEXOSAMINIDASEHexosaminidase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / BETA-N-ACETYLHEXOSAMINIDASE / CHITINOLYSIS / A/B(TIM)-BARREL / SITE DIRECTED MUTAGENESIS / SUBSTRATE NUCLEOPHILE STABILIZER MUTATION
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / chitin catabolic process / polysaccharide binding / polysaccharide catabolic process / periplasmic space
Similarity search - Function
Chitobiase/beta-hexosaminidases, N-terminal domain / Chitobiase C-terminal domain / Putative carbohydrate binding domain / Chitobiase/beta-hexosaminidase C-terminal domain / Putative carbohydrate binding domain / Immunoglobulin-like - #290 / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like ...Chitobiase/beta-hexosaminidases, N-terminal domain / Chitobiase C-terminal domain / Putative carbohydrate binding domain / Chitobiase/beta-hexosaminidase C-terminal domain / Putative carbohydrate binding domain / Immunoglobulin-like - #290 / 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, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / CBM2, carbohydrate-binding domain superfamily / Beta-hexosaminidase-like, domain 2 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPrag, G. / Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K. / Oppenheim, A.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540.
Authors: Prag, G. / Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K. / Oppenheim, A.B.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Bacterial Chitobiase Structure Provides Insight Into Catalytic Mechanism and the Basis of Tay-Sachs Disease
Authors: Tews, I. / Perrakis, A. / Oppenheim, A. / Dauter, Z. / Wilson, K.S. / Vorgias, C.E.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7506
Polymers95,9411
Non-polymers8095
Water14,790821
1
A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules

A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,49912
Polymers191,8822
Non-polymers1,61710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Unit cell
Length a, b, c (Å)108.794, 99.960, 86.308
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-N-ACETYLHEXOSAMINIDASE / Hexosaminidase / N-ACETYL-BETA-D-GLUCOSAMINIDASE / CHITOBIASE


Mass: 95940.930 Da / Num. of mol.: 1
Fragment: MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION
Mutation: D539A
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH DINAG / Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: A9301 / Plasmid: PKK177-3 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q54468, 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 ...Details: CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.3 Mammonium sulfate1reservoir
2100 mMcacodylate1reservoir
340 mg/mlprotein1drop
410 mMdiNAG1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999 / Details: 345 MM IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 76047 / % possible obs: 96.9 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 32832
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 4738 / % possible all: 90.8
Reflection
*PLUS
% possible obs: 86.9 % / Num. measured all: 937195
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 90.8 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
REFMAC/ ARPrefinement
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBB

1qbb


Resolution: 1.8→15 Å / SU B: 2.724 / SU ML: 0.087 / Cross valid method: R-FREE / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7659 10 %RANDOM
Rwork0.171 ---
obs0.183 76047 86.9 %-
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 49 823 7654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0240.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4812
X-RAY DIFFRACTIONp_mcangle_it2.0163
X-RAY DIFFRACTIONp_scbond_it2.5843
X-RAY DIFFRACTIONp_scangle_it3.4964
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1170.12
X-RAY DIFFRACTIONp_singtor_nbd0.1840.5
X-RAY DIFFRACTIONp_multtor_nbd0.2410.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.53
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'REFMAC / ARP' / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it4

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