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- PDB-1y65: Crystal structure of beta-hexosaminidase from Vibrio cholerae in ... -

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Basic information

Entry
Database: PDB / ID: 1y65
TitleCrystal structure of beta-hexosaminidase from Vibrio cholerae in complex with N-acetyl-D-glucosamine to a resolution of 1.85
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / beta-alpha barrel / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of beta-hexosaminidase from Vibrio cholerae in complex with N-acetyl-D-glucosamine to a resolution of 1.85
Authors: Gorman, J. / Shapiro, L.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 3, 2021Group: Structure summary / Category: audit_author / chem_comp
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms
Revision 1.6Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0872
Polymers37,8661
Non-polymers2211
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.524, 81.203, 86.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-hexosaminidase / N-acetyl-beta-glucosaminidase / Beta-N-acetylhexosaminidase


Mass: 37865.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: nagZ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KU37, beta-N-acetylhexosaminidase
#2: 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.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.36 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG 20,000, 0.1 M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 29853 / Num. obs: 29405 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Χ2: 1.012 / Net I/σ(I): 15.9
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.67 / Num. unique all: 2617 / Χ2: 1.058 / % possible all: 89.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.502data extraction
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TR9

1tr9


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.852 / SU ML: 0.087 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1494 5.1 %RANDOM
Rwork0.157 ---
all0.16 29853 --
obs0.157 29328 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--1.99 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 15 466 3040
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01326270.022
X-RAY DIFFRACTIONr_bond_other_d0.00123970.02
X-RAY DIFFRACTIONr_angle_refined_deg1.435521.96
X-RAY DIFFRACTIONr_angle_other_deg1.09455573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8743295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16312624.127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23144115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3241915
X-RAY DIFFRACTIONr_chiral_restr0.0933850.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00529630.02
X-RAY DIFFRACTIONr_gen_planes_other0.0015320.02
X-RAY DIFFRACTIONr_nbd_refined0.215870.2
X-RAY DIFFRACTIONr_nbd_other0.19225240.2
X-RAY DIFFRACTIONr_nbtor_refined0.17212590.2
X-RAY DIFFRACTIONr_nbtor_other0.09113730.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1553450.2
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.08210.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.144180.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.252540.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.171270.2
X-RAY DIFFRACTIONr_mcbond_it1.07421121.5
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A**2)0.1856761.5
X-RAY DIFFRACTIONr_mcangle_it1.10526012
X-RAY DIFFRACTIONr_scbond_it2.28911383
X-RAY DIFFRACTIONr_scangle_it3.119514.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.851-1.8990.2941020.2331769187187.43
1.899-1.950.289990.204197793.343
1.95-2.0060.2751170.208199998.328
2.006-2.0670.2981100.198197999.198
2.067-2.1340.211020.155187199.792
2.134-2.2080.1911050.1461896100
2.208-2.2910.19920.154179199.611
2.291-2.3830.246850.149172599.884
2.383-2.4870.199720.151676100
2.487-2.6070.202740.153162299.815
2.607-2.7450.235730.1541509100
2.745-2.9080.191670.1471466100
2.908-3.1040.219600.151376100
3.104-3.3460.216720.1551283100
3.346-3.6550.177600.1431202100
3.655-4.070.154610.132109499.909
4.07-4.6670.145430.12396399.793
4.667-5.640.183390.15885399.883
5.64-7.6770.252430.189681100
7.677-200.204180.19544998.899

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