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- PDB-6yrp: Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in... -

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Basic information

Entry
Database: PDB / ID: 6yrp
TitleCrystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with JMV-4690 (Cpd 31)
ComponentsMetallo-beta-lactamase VIM-2-like protein
KeywordsHYDROLASE / Metallo-beta-lactamase / triazole-thione inhibitor / antibiotic resistance / carbapenem-hydrolyzing beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / 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 / Chem-PJB / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDocquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: 4-Amino-1,2,4-triazole-3-thione-derived Schiff bases as metallo-beta-lactamase inhibitors.
Authors: Gavara, L. / Sevaille, L. / De Luca, F. / Mercuri, P. / Bebrone, C. / Feller, G. / Legru, A. / Cerboni, G. / Tanfoni, S. / Baud, D. / Cutolo, G. / Bestgen, B. / Chelini, G. / Verdirosa, F. / ...Authors: Gavara, L. / Sevaille, L. / De Luca, F. / Mercuri, P. / Bebrone, C. / Feller, G. / Legru, A. / Cerboni, G. / Tanfoni, S. / Baud, D. / Cutolo, G. / Bestgen, B. / Chelini, G. / Verdirosa, F. / Sannio, F. / Pozzi, C. / Benvenuti, M. / Kwapien, K. / Fischer, M. / Becker, K. / Frere, J.M. / Mangani, S. / Gresh, N. / Berthomieu, D. / Galleni, M. / Docquier, J.D. / Hernandez, J.F.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,49011
Polymers25,5391
Non-polymers95110
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-26 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.140, 79.000, 79.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#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: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8QIQ9

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Non-polymers , 6 types, 131 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PJB / 2-[[[3-(5-methoxy-2-oxidanyl-phenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]amino]methyl]benzoic acid


Mass: 372.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 41.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.95→56.104 Å / Num. all: 14141 / Num. obs: 14141 / % possible obs: 89 % / Redundancy: 3.7 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.102 / Rsym value: 0.089 / Net I/av σ(I): 6.1 / Net I/σ(I): 10 / Num. measured all: 52194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.063.60.3662.1759521050.2050.4220.3663.491.5
2.06-2.183.60.2443.1715219650.1350.2810.244590.9
2.18-2.333.70.194676018490.1050.2180.196.190.4
2.33-2.523.70.1355.4631017090.0740.1550.1358.289.7
2.52-2.763.70.17.2582115700.0550.1150.110.489
2.76-3.083.80.0759.2526514030.040.0850.07512.888.1
3.08-3.563.80.06110.1462812290.0320.0690.06115.987.2
3.56-4.363.80.0658.7396310530.0330.0730.06518.886.3
4.36-6.173.80.0589.430608040.030.0650.05820.284.6
6.17-34.073.60.0441216404540.0250.0510.04421.282.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREP10.2.31phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.95→34.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.235 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 707 5 %RANDOM
Rwork0.1744 ---
obs0.1775 13432 88.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 21.723 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.95→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 53 121 1902
Biso mean--32.2 29.82 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131806
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171653
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6622449
X-RAY DIFFRACTIONr_angle_other_deg1.2921.5813802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3615221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28121.8686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3541511
X-RAY DIFFRACTIONr_chiral_restr0.070.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 51 -
Rwork0.242 1010 -
all-1061 -
obs--90.76 %

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