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- PDB-5utq: Crystal structure of Burkholderia cenocepacia family 3 glycoside ... -

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Basic information

Entry
Database: PDB / ID: 5utq
TitleCrystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to PUGNAc
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Glycoside hydrolase / GH / family 3 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / 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-OAN / Beta-hexosaminidase / Beta-hexosaminidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVadlamani, G. / Mark, B.L.
CitationJournal: Protein Sci. / Year: 2017
Title: Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.
Authors: Vadlamani, G. / Stubbs, K.A. / Desire, J. / Bleriot, Y. / Vocadlo, D.J. / Mark, B.L.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1355
Polymers76,2342
Non-polymers9023
Water6,467359
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6653
Polymers38,1171
Non-polymers5492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4702
Polymers38,1171
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.670, 87.670, 66.700
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-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, A3203_21235, WL84_04775 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A125HFC0, UniProt: B4EA43*PLUS, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc


Mass: 353.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N3O7
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 1.87 Å3/Da / Density % sol: 34.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30-32% PEG8000, 0.1 M MES, pH 6.2-6.8 / PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→43.83 Å / Num. obs: 28278 / % possible obs: 99.4 % / Redundancy: 2.2 % / CC1/2: 0.966 / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2 / Num. unique obs: 2423 / CC1/2: 0.647 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2236)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4G6C

4g6c


Resolution: 2.2→36.302 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.48
RfactorNum. reflection% reflection
Rfree0.2113 --
Rwork0.1655 --
obs-28239 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→36.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 62 359 5431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025190
X-RAY DIFFRACTIONf_angle_d0.6027062
X-RAY DIFFRACTIONf_dihedral_angle_d15.1593092
X-RAY DIFFRACTIONf_chiral_restr0.039828
X-RAY DIFFRACTIONf_plane_restr0.003918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.29651390.23581854X-RAY DIFFRACTION99
2.255-2.3160.28091470.21271863X-RAY DIFFRACTION99
2.316-2.38410.23561430.2021875X-RAY DIFFRACTION99
2.3841-2.46110.26181380.19591872X-RAY DIFFRACTION100
2.4611-2.5490.24291380.18941876X-RAY DIFFRACTION99
2.549-2.6510.24281450.17711866X-RAY DIFFRACTION100
2.651-2.77160.26591450.18491874X-RAY DIFFRACTION100
2.7716-2.91770.20731510.18391895X-RAY DIFFRACTION100
2.9177-3.10040.22431450.17461858X-RAY DIFFRACTION100
3.1004-3.33970.19711470.15911896X-RAY DIFFRACTION100
3.3397-3.67550.19311410.14841882X-RAY DIFFRACTION99
3.6755-4.20660.17841370.12921890X-RAY DIFFRACTION99
4.2066-5.29730.16661410.12911880X-RAY DIFFRACTION98

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