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- PDB-1qba: BACTERIAL CHITOBIASE, GLYCOSYL HYDROLASE FAMILY 20 -

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Basic information

Entry
Database: PDB / ID: 1qba
TitleBACTERIAL CHITOBIASE, GLYCOSYL HYDROLASE FAMILY 20
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 / MIR / Resolution: 1.85 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.
#2: Journal: Serratia Marcescens Chitobiase / Year: 1996
Authors: Tews, I.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITOBIASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3085
Polymers95,9241
Non-polymers3844
Water13,890771
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 / BETA-N-ACETYLHEXOSAMINIDASE / N-ACETYL-BETA-D-GLUCOSAMINIDASE


Mass: 95923.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria)
Description: PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION
Plasmid: PEMBL18 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): A5484 / References: UniProt: Q54468, beta-N-acetylhexosaminidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 771 / 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., vapor diffusion - hanging drop
Temp details: room temp
Crystal
*PLUS
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: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 1994 / Details: SEGMENTED TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→10 Å / Num. obs: 82854 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Num. obs: 83596
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
PROLSQrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.85→10 Å / Cross valid method: R-FREE / σ(F): -4
Details: RESIDUES 155 AND 156: THERE IS ONLY WEAK DENSITY AND THESE RESIDUES MAY FORM (TWO OR MORE) ALTERNATIVE LOOP CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 8303 10 %X-PLOR
Rwork0.139 ---
obs0.146 82584 99.9 %-
all-82854 --
Displacement parametersBiso mean: 17.96 Å2
Refine analyzeLuzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 20 771 7598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0260.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.92
X-RAY DIFFRACTIONp_mcangle_it2.73
X-RAY DIFFRACTIONp_scbond_it4.83
X-RAY DIFFRACTIONp_scangle_it7.24
X-RAY DIFFRACTIONp_plane_restr0.0230.02
X-RAY DIFFRACTIONp_chiral_restr0.1210.1
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1790.3
X-RAY DIFFRACTIONp_planar_tor4.66
X-RAY DIFFRACTIONp_staggered_tor17.420
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.630
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.963 Å2

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