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- PDB-1qbb: BACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG) -

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Basic information

Entry
Database: PDB / ID: 1qbb
TitleBACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG)
ComponentsCHITOBIASE
KeywordsGLYCOSYL HYDROLASE / CHITOBIASE / CHITINOLYSIS / BA8-BARREL
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / chitin catabolic process / polysaccharide binding / polysaccharide catabolic process / periplasmic space / membrane
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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / CBM2, carbohydrate-binding domain superfamily / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / 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: 2 Å
AuthorsTews, I. / Perrakis, A. / Oppenheim, A. / Dauter, Z. / Wilson, K.S. / Vorgias, C.E.
Citation
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.
#1: Journal: Gene / Year: 1996
Title: N-Acetylglucosaminidase (Chitobiase) from Serratia Marcescens: Gene Sequence, and Protein Production and Purification in Escherichia Coli
Authors: Tews, I. / Vincentelli, R. / Vorgias, C.E.
#3: Journal: Mol.Gen.Genet. / Year: 1989
Title: Cloning of the Gene Coding for Chitobiase of Serratia Marcescens
Authors: Kless, H. / Sitrit, Y. / Chet, I. / Oppenheim, A.B.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1978
Title: The Crystal Structure of a B-(1,4) Linked Disaccharide A-N,N'Diacetylchitobiose Monohydrate
Authors: Mo, F. / Jensen, L.H.
#2: Journal: Serratia Marcescens Chitobiase / Year: 1996
Authors: Tews, I.
History
DepositionJun 7, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITOBIASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7336
Polymers95,9241
Non-polymers8095
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.700, 99.900, 87.700
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 CHITOBIASE / N-ACETYL-BETA-D-GLUCOSAMINIDASE


Mass: 95923.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CHITOBIOSE (DINAG) / Source: (gene. exp.) Serratia marcescens (bacteria)
Description: PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1 - 27 CLEAVED OFF DURING MATURATION
Plasmid: PEMBL18 / Production host: Escherichia coli (E. coli) / Strain (production host): A5484 / 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
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 44.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID ...Details: CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID CHITOBIOSE WAS ADDED TO THE MOTHER LIQUOR TO MAKE UP HIGH CONCENTRATED STOCK SOLUTION, 0.5 TO 1.0 MICRO LITERS OF THE STOCK SOLUTION WERE ADDED TO THE CRYSTALLISATION DROP CONTAINING CRYSTALS. THE CRYSTALS WERE MOUNTED IMMEDIATELY IN GLASS CAPILLARY. EXPOSURE TIME WAS LIMITED TO 10 MINUTES OR LESS. THESE CRYSTALS: 4 MINS 50 SECS. THE CHITOBIOSE WAS SUPPLIED BY SIGMA., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
161.5 %ammonium salfate11
21.5 %isopropanol11
3100 mMcacodylate11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1994 / Details: SEGMENTED TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.99→15 Å / Num. obs: 66148 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBA

1qba


Resolution: 2→15 Å / Cross valid method: R-FREE / σ(F): -4
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6509 10 %RANDOM
Rwork0.151 ---
obs0.148 66148 99.7 %-
all-66148 --
Displacement parametersBiso mean: 14.3 Å2
Refine analyzeLuzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6795 0 50 542 7387
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0280.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.22
X-RAY DIFFRACTIONp_mcangle_it33
X-RAY DIFFRACTIONp_scbond_it53
X-RAY DIFFRACTIONp_scangle_it7.44
X-RAY DIFFRACTIONp_plane_restr0.0240.02
X-RAY DIFFRACTIONp_chiral_restr0.1330.1
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1630.3
X-RAY DIFFRACTIONp_planar_tor4.86
X-RAY DIFFRACTIONp_staggered_tor17.720
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.430
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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