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- PDB-3gsm: Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Va... -

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Basic information

Entry
Database: PDB / ID: 3gsm
TitleVibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / glycoside hydrolases / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Glycosidase / Peptidoglycan synthesis
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / beta-N-acetylglucosaminidase activity / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / response to antibiotic / cytosol
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 ...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
Chem-VPU / Beta-hexosaminidase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBalcewich, M.D. / Mark, B.L.
CitationJournal: Protein Sci. / Year: 2009
Title: Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
Authors: Balcewich, M.D. / Stubbs, K.A. / He, Y. / James, T.W. / Davies, G.J. / Vocadlo, D.J. / Mark, B.L.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,2944
Polymers37,7151
Non-polymers5803
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.980, 86.440, 86.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsone biological molecule in the asymmetric unit

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Components

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


Mass: 37714.848 Da / Num. of mol.: 1 / Mutation: E19A, Q22A, K54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: Vibrio cholerae O1 biovar eltor str. N16961 / Gene: family 3 glycoside hydrolase NagZ, nagZ, VC_0692 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD HTE / References: UniProt: Q9KU37, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-VPU / [[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(pentanoylamino)oxan-2-ylidene]amino] N-phenylcarbamate / N-Valeryl-PUGNAc


Mass: 395.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25N3O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 13% PEG 20,000, 10% glycerol, 100mM Bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→61.08 Å / Num. all: 14609 / Num. obs: 14482 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.97 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OXN

2oxn


Resolution: 2.4→61.08 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.329 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The VPU residue, bound inhibitor N-valeryl PUGNAc, has missing atoms: OAQ CAP OAR NAO CAS CAT CAU CAV CAW CAX. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27174 727 5 %RANDOM
Rwork0.20937 ---
obs0.2125 13755 99.14 %-
all-15335 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---1.32 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.4→61.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 30 128 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222609
X-RAY DIFFRACTIONr_bond_other_d00.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.973521
X-RAY DIFFRACTIONr_angle_other_deg0.63235525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70523.984123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25715430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212917
X-RAY DIFFRACTIONr_gen_planes_other00.02526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.51604
X-RAY DIFFRACTIONr_mcbond_other0.0911.5663
X-RAY DIFFRACTIONr_mcangle_it0.99122549
X-RAY DIFFRACTIONr_scbond_it1.46131005
X-RAY DIFFRACTIONr_scangle_it2.4994.5972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 58 -
Rwork0.28 979 -
obs--100 %

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