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- PDB-7ove: Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 7ove
TitleCrystal structure of the VIM-2 acquired metallo-beta-Lactamase in Complex with compound 10 (JMV-7210)
ComponentsMetallo-beta-lactamase VIM-2-like protein
KeywordsHYDROLASE / metallo-beta-Lactamase / VIM-2 / triazole-thione / inhibitor / zinc
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
ACETATE ION / Unknown ligand / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTassone, G. / Benvenuti, M. / Verdirosa, F. / Sannio, F. / Mangani, S. / Docquier, J.D. / Pozzi, C. / Marcoccia, F.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: 1,2,4-Triazole-3-thione compounds with a 4-ethyl alkyl/aryl sulfide substituent are broad-spectrum metallo-beta-lactamase inhibitors with re-sensitization activity.
Authors: Legru, A. / Verdirosa, F. / Hernandez, J.F. / Tassone, G. / Sannio, F. / Benvenuti, M. / Conde, P.A. / Bossis, G. / Thomas, C.A. / Crowder, M.W. / Dillenberger, M. / Becker, K. / Pozzi, C. / ...Authors: Legru, A. / Verdirosa, F. / Hernandez, J.F. / Tassone, G. / Sannio, F. / Benvenuti, M. / Conde, P.A. / Bossis, G. / Thomas, C.A. / Crowder, M.W. / Dillenberger, M. / Becker, K. / Pozzi, C. / Mangani, S. / Docquier, J.D. / Gavara, L.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)25,8547
Polymers25,5391
Non-polymers3146
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-109 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.116, 78.133, 79.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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 / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 18.015 Da / Num. of mol.: 153 / 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: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M cacodilate (pH 6.5), 5 mM DTT , 0.2 M 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: 0.979499 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: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.92→55.66 Å / Num. obs: 16503 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.073 / Rrim(I) all: 0.144 / Net I/σ(I): 9.5
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2369 / CC1/2: 0.807 / Rpim(I) all: 0.41 / Rrim(I) all: 0.825 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SP7

6sp7


Resolution: 1.92→51.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.748 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 875 5.3 %RANDOM
Rwork0.19 ---
obs0.193 15627 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.5 Å2 / Biso mean: 27.943 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2266 Å0.2266 Å
Refinement stepCycle: final / Resolution: 1.92→51.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 26 155 1913
Biso mean--41.58 34.58 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121795
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6412455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61221.8686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87215250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2571511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021408
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 60 -
Rwork0.255 1137 -
all-1197 -
obs--100 %

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