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- PDB-6tm9: VIM-2_1cc-. Triazole inhibitors with promising inhibitor effects ... -

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Basic information

Entry
Database: PDB / ID: 6tm9
TitleVIM-2_1cc-. Triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases
ComponentsBeta-lactamase class B VIM-2
KeywordsANTIBIOTIC / Metallo-beta-lactamase inhibitor / NH-triazole / inhibition properties / crystal structure.
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-9NW / HYDROXIDE ION / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsLeiros, H.-K.S.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273332/2018 Norway
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Structural studies of triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-beta-lactamases.
Authors: Muhammad, Z. / Skagseth, S. / Boomgaren, M. / Akhter, S. / Frohlich, C. / Ismael, A. / Christopeit, T. / Bayer, A. / Leiros, H.S.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9195
Polymers28,3531
Non-polymers5664
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-83 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.347, 44.343, 60.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21A-801-

HOH

31A-851-

HOH

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Class B carbapenemase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 28352.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Zn and OH- are bound to the Enzme / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-9NW / 2,5-bis(chloranyl)-~{N}-[[5-[(cyclohexylamino)methyl]-2~{H}-1,2,3-triazol-4-yl]methyl]benzenesulfonamide


Mass: 418.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21Cl2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 22-27% polyethylene glycol (PEG) 3350 and 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.07→38.26 Å / Num. obs: 115206 / % possible obs: 97.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 10.41 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.4
Reflection shellResolution: 1.07→1.0968 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 0

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACX

5acx


Resolution: 1.07→38.24 Å / SU ML: 0.0916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1575 2000 1.74 %
Rwork0.1381 113205 -
obs0.1385 115205 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.88 Å2
Refinement stepCycle: LAST / Resolution: 1.07→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 29 353 2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01671988
X-RAY DIFFRACTIONf_angle_d1.46682753
X-RAY DIFFRACTIONf_chiral_restr0.1021304
X-RAY DIFFRACTIONf_plane_restr0.0108375
X-RAY DIFFRACTIONf_dihedral_angle_d20.882722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.10.24851340.24347572X-RAY DIFFRACTION92.92
1.1-1.130.21891370.21517786X-RAY DIFFRACTION94.81
1.13-1.160.24311380.19737810X-RAY DIFFRACTION95.46
1.16-1.20.21351400.18817905X-RAY DIFFRACTION96.51
1.2-1.240.18921410.1617962X-RAY DIFFRACTION97.29
1.24-1.290.15791420.15018056X-RAY DIFFRACTION98.47
1.29-1.350.15161440.13738170X-RAY DIFFRACTION99.02
1.35-1.420.14681450.12458177X-RAY DIFFRACTION99.44
1.42-1.510.13851440.11828178X-RAY DIFFRACTION99.39
1.51-1.620.14111450.11658232X-RAY DIFFRACTION99.64
1.62-1.790.13681470.11838277X-RAY DIFFRACTION99.65
1.79-2.050.1491460.11598285X-RAY DIFFRACTION99.67
2.05-2.580.13491480.12558307X-RAY DIFFRACTION98.84
2.58-38.240.16311490.14448488X-RAY DIFFRACTION97.43

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