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- PDB-6dte: GlcNAc-inspired cyclophellitol bound to NagZ -

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Basic information

Entry
Database: PDB / ID: 6dte
TitleGlcNAc-inspired cyclophellitol bound to NagZ
ComponentsBeta-hexosaminidaseHexosaminidase
KeywordsHYDROLASE / Antibiotic potentiator / Antibiotic adjuvant / NagZ / glycosides / epoxide / GlcNAc / Antibiotic resistance / AmpC
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 / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / 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
Chem-H9J / Beta-hexosaminidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsMark, B.L. / Winogrodzki, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)201603PJT-361930 Canada
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to beta-lactams in Pseudomonas aeruginosa.
Authors: Ho, L.A. / Winogrodzki, J.L. / Debowski, A.W. / Madden, Z. / Vocadlo, D.J. / Mark, B.L. / Stubbs, K.A.
History
DepositionJun 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-hexosaminidase
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8124
Polymers76,2342
Non-polymers5782
Water15,187843
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4062
Polymers38,1171
Non-polymers2891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4062
Polymers38,1171
Non-polymers2891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.910, 88.140, 67.310
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38116.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Gene: nagZ, A8E72_12990, A8F51_10310, A8F55_30255, BCN122_I0864, BCN122_I2678, BCN122_II1911, UE95_02480
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A125HFC0, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-H9J / 2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide


Mass: 289.206 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H14F3NO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 1.93 Å3/Da / Density % sol: 36.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30-32% PEG8000, 0.1M MES pH 6.6-6.8 / PH range: 6.6-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.929→67.27 Å / Num. obs: 42981 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.3
Reflection shellResolution: 1.929→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2882 / CC1/2: 0.833 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3139: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6C

4g6c


Resolution: 1.929→40.226 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2010 4.68 %Random selection
Rwork0.1535 ---
obs0.1557 42953 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.929→40.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 36 843 5983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035288
X-RAY DIFFRACTIONf_angle_d0.6537213
X-RAY DIFFRACTIONf_dihedral_angle_d16.763165
X-RAY DIFFRACTIONf_chiral_restr0.04848
X-RAY DIFFRACTIONf_plane_restr0.004940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.97720.25881460.21272920X-RAY DIFFRACTION99
1.9772-2.03070.25491310.19542886X-RAY DIFFRACTION100
2.0307-2.09050.22181470.17932914X-RAY DIFFRACTION100
2.0905-2.15790.25961440.17012895X-RAY DIFFRACTION100
2.1579-2.2350.2261380.16182935X-RAY DIFFRACTION100
2.235-2.32450.18551440.15762928X-RAY DIFFRACTION100
2.3245-2.43030.20571470.15442880X-RAY DIFFRACTION100
2.4303-2.55840.23211450.16012940X-RAY DIFFRACTION100
2.5584-2.71870.21581370.16072948X-RAY DIFFRACTION100
2.7187-2.92850.20321440.16012905X-RAY DIFFRACTION100
2.9285-3.22310.21441370.15222926X-RAY DIFFRACTION100
3.2231-3.68920.16831480.13452938X-RAY DIFFRACTION100
3.6892-4.64690.16121470.11652949X-RAY DIFFRACTION100
4.6469-40.23460.1771550.15052979X-RAY DIFFRACTION100

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