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- PDB-6tmb: VIM-2_1di-Triazole inhibitors with promising inhibitor effects ag... -

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Basic information

Entry
Database: PDB / ID: 6tmb
TitleVIM-2_1di-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


antibiotic catabolic process / beta-lactamase / 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-9OB / IODIDE ION / HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLeiros, H.-K.S. / Christopeit, T.
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 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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_residues
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-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,75816
Polymers56,7062
Non-polymers1,05314
Water11,854658
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6377
Polymers28,3531
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1219
Polymers28,3531
Non-polymers7688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.590, 79.026, 67.235
Angle α, β, γ (deg.)90.000, 130.094, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 672 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-9OB / ~{N}-[[5-[[(phenylmethyl)amino]methyl]-1~{H}-1,2,3-triazol-4-yl]methyl]benzenesulfonamide


Mass: 357.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.8 Å3/Da / Density % sol: 31.76 %
Crystal growTemperature: 295 K / Method: liquid diffusion / Details: 22-27% 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: ID29 / Wavelength: 0.983998 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983998 Å / Relative weight: 1
ReflectionResolution: 1.5→33.6 Å / Num. obs: 61683 / % possible obs: 95.8 % / Redundancy: 11.5 % / Biso Wilson estimate: 13.61 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 0 / % possible all: 98

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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: 5LSC

5lsc


Resolution: 1.5→31.6 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5909
RfactorNum. reflection% reflection
Rfree0.1676 3067 4.97 %
Rwork0.1392 --
obs0.1407 61683 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 38 658 4162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213808
X-RAY DIFFRACTIONf_angle_d1.08835244
X-RAY DIFFRACTIONf_chiral_restr0.0661591
X-RAY DIFFRACTIONf_plane_restr0.0081704
X-RAY DIFFRACTIONf_dihedral_angle_d20.38471368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22281400.19952749X-RAY DIFFRACTION97.7
1.52-1.550.20761400.18812721X-RAY DIFFRACTION98.28
1.55-1.580.2181330.18892692X-RAY DIFFRACTION97.89
1.58-1.60.21511300.18092727X-RAY DIFFRACTION97.98
1.6-1.630.18281510.16662708X-RAY DIFFRACTION98.01
1.63-1.670.20641370.16612695X-RAY DIFFRACTION97.99
1.67-1.70.18671420.16092673X-RAY DIFFRACTION96.74
1.7-1.740.18991590.15872689X-RAY DIFFRACTION97.84
1.74-1.790.18451400.15342734X-RAY DIFFRACTION97.89
1.79-1.840.19931470.15182699X-RAY DIFFRACTION97.27
1.84-1.890.1791550.14662653X-RAY DIFFRACTION96.79
1.89-1.950.18131450.14632635X-RAY DIFFRACTION95.57
1.95-2.020.17351300.13722676X-RAY DIFFRACTION95.67
2.02-2.10.16661270.1322685X-RAY DIFFRACTION96.3
2.1-2.20.15151300.12942685X-RAY DIFFRACTION96.11
2.2-2.310.17421500.13212605X-RAY DIFFRACTION94.35
2.31-2.460.1661100.12912645X-RAY DIFFRACTION94.19
2.46-2.650.16811380.12812580X-RAY DIFFRACTION92.73
2.65-2.910.17761400.13082636X-RAY DIFFRACTION94.65
2.91-3.330.13851610.12432581X-RAY DIFFRACTION93.33
3.34-4.20.13921400.11572562X-RAY DIFFRACTION91.38
4.2-33.60.15481220.14582586X-RAY DIFFRACTION90.39

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