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- PDB-5lca: VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-(3-(trifluor... -

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Basic information

Entry
Database: PDB / ID: 5lca
TitleVIM-2 metallo-beta-lactamase in complex with 3-oxo-2-(3-(trifluoromethyl)phenyl)isoindoline-4-carboxylic acid (compound 17)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B06 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsLi, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2017
Title: NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors.
Authors: Li, G.B. / Abboud, M.I. / Brem, J. / Someya, H. / Lohans, C.T. / Yang, S.Y. / Spencer, J. / Wareham, D.W. / McDonough, M.A. / Schofield, C.J.
History
DepositionJun 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2659
Polymers28,3531
Non-polymers9138
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-83 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.487, 65.313, 70.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 ...Beta-lactamase / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 28352.836 Da / Num. of mol.: 1
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
Plasmid: OPINF
Details (production host): OPINF VECTOR BASED ON PTRIEX VECTOR
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B06 / 3-oxidanylidene-2-[3-(trifluoromethyl)phenyl]-1~{H}-isoindole-4-carboxylic acid


Mass: 321.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10F3NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 1.82 Å3/Da / Density % sol: 32.4 % / Description: rhombohedra plates
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.25 M Magnesium formate, 22.0% (v/v) Polyethylene glycol 3350, 5 mM 3-oxo-2-(3-(trifluoromethyl)phenyl)isoindoline-4-carboxylic acid, 16 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 13, 2016 / Details: OSMIC HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 14437 / % possible obs: 98.2 % / Redundancy: 7 % / Biso Wilson estimate: 15.27 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 1.07 / Net I/av σ(I): 32.62 / Net I/σ(I): 31.7 / Num. measured all: 100610
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.93-270.0932.4197.4
2-2.0870.081197.6
2.08-2.177.10.073197.1
2.17-2.297.10.068197.4
2.29-2.437.10.061198.3
2.43-2.6270.056198.8
2.62-2.8870.046198.8
2.88-3.370.041199.4
3.3-4.166.90.034199.2
4.16-506.50.03198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.86 Å23.99 Å
Translation5.86 Å23.99 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
CrystalCleardata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c1d

4c1d


Resolution: 1.93→23.99 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.11
RfactorNum. reflection% reflection
Rfree0.1697 1438 9.98 %
Rwork0.1302 --
obs0.1342 14407 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.6 Å2 / Biso mean: 17.3166 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 1.93→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 55 149 1858
Biso mean--31.22 28.31 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091751
X-RAY DIFFRACTIONf_angle_d0.6472381
X-RAY DIFFRACTIONf_chiral_restr0.049267
X-RAY DIFFRACTIONf_plane_restr0.004308
X-RAY DIFFRACTIONf_dihedral_angle_d14.762998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.99890.15721370.11921246138397
1.9989-2.07890.16381360.11281268140498
2.0789-2.17350.15941430.11611253139697
2.1735-2.2880.15091410.12141266140797
2.288-2.43120.15481480.12351271141998
2.4312-2.61870.18561400.12561307144799
2.6187-2.88180.16711410.12911297143899
2.8818-3.29790.15731460.12531315146199
3.2979-4.15150.15731490.12441344149399
4.1515-23.99170.20621570.16121402155999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.540.9406-0.52865.7636-0.80353.61190.0596-0.30680.03440.6868-0.00160.0382-0.2506-0.0753-0.09270.1041-0.00830.01060.1452-0.00590.0353-7.020118.5302-2.3421
22.4471-0.5436-0.36413.77880.16051.85140.07260.02820.1096-0.0458-0.0374-0.0293-0.12250.0152-0.01080.0666-0.01470.00260.0538-0.00890.0405-2.904218.2775-9.0457
30.71-0.3280.42031.4563-1.29923.04030.0056-0.05860.00220.0602-0.0012-0.02730.00380.0356-0.00970.0553-0.01450.00570.0848-0.01150.09092.48717.9217-8.6523
43.27850.43450.06924.5437-0.2982.95330.06940.11120.0107-0.0534-0.1575-0.203-0.060.11510.07020.0429-0.00430.02350.09580.00290.10057.91918.2362-19.9939
52.03640.5735-0.23191.3684-0.42960.83-0.01450.18-0.2509-0.03190.018-0.01450.1259-0.0342-0.0110.1004-0.00550.00670.0903-0.02670.0855-2.71769.7714-20.669
63.9777-0.2491-1.31830.7667-0.27423.7288-0.06570.28410.4666-0.0511-0.0940.0208-0.2964-0.1146-0.00010.1255-0.0114-0.02330.14360.01630.1579-15.37823.0058-21.743
72.03030.9561-0.67673.2909-4.67057.8246-0.01450.5072-0.1901-0.51530.08850.370.5165-0.4147-0.12690.1404-0.0002-0.02630.2419-0.05110.1391-14.91710.3561-27.5574
83.55560.45650.394.85141.9594.9286-0.0271-0.0139-0.24980.3862-0.00330.2820.3194-0.1730.0390.0591-0.0050.01180.10560.00120.0857-14.494611.1105-12.7048
94.5035-0.9930.64277.3846-4.85223.40480.03090.3029-0.0122-0.28330.05250.15110.1002-0.2581-0.14020.0993-0.0036-0.00240.1394-0.010.1081-21.26116.6408-22.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 52 )A39 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 88 )A53 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 122 )A89 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 146 )A123 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 199 )A147 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 215 )A200 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 229 )A216 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 245 )A230 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 260 )A246 - 260

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