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- PDB-8a4m: Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 8a4m
TitleCrystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 8 (JMV-7061)
ComponentsMetallo-beta-lactamase VIM-2-like protein
KeywordsHYDROLASE / metallo-beta-Lactamase / VIM-2 / triazole-thione / inhibitor / zinc
Function / homology
Function and homology information


: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-L2R / Metallo-beta-lactamase VIM-2-like protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTassone, G. / Benvenuti, M. / Verdirosa, F. / Corsica, G. / Sannio, F. / Docquier, J.D. / Pozzi, C. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-beta-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates.
Authors: Legru, A. / Verdirosa, F. / Vo-Hoang, Y. / Tassone, G. / Vascon, F. / Thomas, C.A. / Sannio, F. / Corsica, G. / Benvenuti, M. / Feller, G. / Coulon, R. / Marcoccia, F. / Devente, S.R. / ...Authors: Legru, A. / Verdirosa, F. / Vo-Hoang, Y. / Tassone, G. / Vascon, F. / Thomas, C.A. / Sannio, F. / Corsica, G. / Benvenuti, M. / Feller, G. / Coulon, R. / Marcoccia, F. / Devente, S.R. / Bouajila, E. / Piveteau, C. / Leroux, F. / Deprez-Poulain, R. / Deprez, B. / Licznar-Fajardo, P. / Crowder, M.W. / Cendron, L. / Pozzi, C. / Mangani, S. / Docquier, J.D. / Hernandez, J.F. / Gavara, L.
History
DepositionJun 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3067
Polymers25,5391
Non-polymers7676
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.883, 78.429, 80.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

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Components

#1: Protein Metallo-beta-lactamase VIM-2-like protein


Mass: 25539.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM / Plasmid: pET9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-L2R / (2~{S})-2-[bis(1~{H}-imidazol-4-ylmethyl)amino]-5-(3-phenyl-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl)pentanoic acid


Mass: 452.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.78 Å3/Da / Density % sol: 30.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M cacodilate pH 6.5, 5mM DTT, 0.2M Na Acetate, 26% peg 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→56.02 Å / Num. obs: 15131 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 13.5
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2138 / CC1/2: 0.833 / Rpim(I) all: 0.272 / Rrim(I) all: 0.668 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OVF

7ovf


Resolution: 1.98→51.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.06 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 704 4.7 %RANDOM
Rwork0.1986 ---
obs0.2014 14426 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.43 Å2 / Biso mean: 35.718 Å2 / Biso min: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.2476 Å
Refinement stepCycle: final / Resolution: 1.98→51.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 43 95 1836
Biso mean--49.4 43.1 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121778
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6542435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55821.89979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4991510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021381
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 44 -
Rwork0.298 1032 -
all-1076 -
obs--98.81 %

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