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

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Basic information

Entry
Database: PDB / ID: 5utr
TitleCrystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Glycoside hydrolase / family 3 / NagZ / 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-8MP / Beta-hexosaminidase / Beta-hexosaminidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.2Jan 17, 2018Group: 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)76,6984
Polymers76,2342
Non-polymers4652
Water11,746652
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3492
Polymers38,1171
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3492
Polymers38,1171
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.660, 87.820, 66.970
Angle α, β, γ (deg.)90.00, 91.92, 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-8MP / N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide


Mass: 232.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 1.88 Å3/Da / Density % sol: 34.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30-32% PEG8000, 0.1M MES pH 6.2-6.8 / PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.033 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→66.93 Å / Num. obs: 30692 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2532 / CC1/2: 0.889 / % possible all: 100

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Processing

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

4g6c


Resolution: 2.15→66.93 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.46
RfactorNum. reflection% reflection
Rfree0.1899 --
Rwork0.1393 --
obs-30672 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→66.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 32 652 5793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025282
X-RAY DIFFRACTIONf_angle_d0.6217190
X-RAY DIFFRACTIONf_dihedral_angle_d16.3053169
X-RAY DIFFRACTIONf_chiral_restr0.04843
X-RAY DIFFRACTIONf_plane_restr0.003939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21940.22821440.16012632X-RAY DIFFRACTION100
2.2194-2.29870.2331470.16052613X-RAY DIFFRACTION100
2.2987-2.39080.22251460.15532650X-RAY DIFFRACTION100
2.3908-2.49960.22321440.15412612X-RAY DIFFRACTION100
2.4996-2.63140.21781420.15072634X-RAY DIFFRACTION100
2.6314-2.79630.20391490.15122631X-RAY DIFFRACTION100
2.7963-3.01220.19031490.1522642X-RAY DIFFRACTION100
3.0122-3.31530.18621470.13722646X-RAY DIFFRACTION100
3.3153-3.7950.15421430.12182649X-RAY DIFFRACTION100
3.795-4.78110.15341490.11242661X-RAY DIFFRACTION100

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