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- PDB-5lch: VIM-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3-met... -

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Basic information

Entry
Database: PDB / ID: 5lch
TitleVIM-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 42)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6TU / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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 21, 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)28,8074
Polymers28,3531
Non-polymers4543
Water4,216234
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-82 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.870, 67.840, 40.350
Angle α, β, γ (deg.)90.000, 91.750, 90.000
Int Tables number4
Space group name H-MP1211

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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
Details: (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindoline-4-carboxylic acid
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 VECTOR BASED ON PTRIEX VECTOR / Details (production host): PLASMID DERIVED NON-GENOMIC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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-6TU / (1~{S})-2-(3-methoxyphenyl)-3-oxidanylidene-1-prop-2-enyl-1~{H}-isoindole-4-carboxylic acid


Mass: 323.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium Formate, 24.5% (v/v) Polyethylene glycol 3350, 1 mM Tris(2-carboxyethyl)phosphine, 5 mM (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindoline-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: May 25, 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: 1.94→20.17 Å / Num. obs: 15884 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 10.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Net I/σ(I): 14.6 / Num. measured all: 49856 / Scaling rejects: 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.94-1.992.30.117199.1
8.89-20.173.40.031193.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å20.17 Å
Translation1.94 Å20.17 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA0.5.17data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1D

4c1d


Resolution: 1.94→20.165 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.01
RfactorNum. reflection% reflection
Rfree0.1612 1583 9.98 %
Rwork0.1253 --
obs0.1289 15867 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.12 Å2 / Biso mean: 13.5849 Å2 / Biso min: 3.18 Å2
Refinement stepCycle: final / Resolution: 1.94→20.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 26 236 1976
Biso mean--19.17 23.4 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131843
X-RAY DIFFRACTIONf_angle_d0.8162521
X-RAY DIFFRACTIONf_chiral_restr0.053283
X-RAY DIFFRACTIONf_plane_restr0.005333
X-RAY DIFFRACTIONf_dihedral_angle_d11.1231066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9401-2.00270.19741380.13481287142599
2.0027-2.07420.16871450.12721288143398
2.0742-2.15710.17811410.12551254139598
2.1571-2.25520.1541440.12411298144299
2.2552-2.37390.1511470.12221296144399
2.3739-2.52240.16461450.114313041449100
2.5224-2.71670.16371410.119512881429100
2.7167-2.98930.16731470.125512871434100
2.9893-3.42010.14291440.126613311475100
3.4201-4.3020.1471460.118913061452100
4.302-20.16660.17141450.137413451490100
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)
11.92551.5831-0.22283.5627-0.84820.91670.07210.4044-0.0905-0.60650.0271-0.53570.1030.07560.05270.1550.05730.11950.16440.05290.190750.5456-59.555753.5373
23.38483.38252.22127.50114.37274.9111-0.05960.03390.0632-0.15630.012-0.0662-0.01210.07270.06730.01470.00010.01340.07020.0140.033447.0162-55.287355.4577
31.146-0.2950.18611.1654-0.21241.3278-0.0464-0.04450.06010.02270.0005-0.0967-0.03740.03280.02310.0327-0.00680.00030.0486-0.00030.04740.0784-50.778561.4818
46.96580.9942-3.9140.1995-0.392.7123-0.28410.0934-0.4309-0.06490.0111-0.05110.5109-0.09970.25130.117-0.0161-0.00370.1157-0.0080.065834.0823-59.063944.3852
58.20644.73210.32137.70780.08062.7152-0.19350.20130.4427-0.23860.17660.325-0.319-0.2748-0.00420.0980.0345-0.00690.10730.01280.051130.1003-45.479744.8963
62.9316-0.6108-0.08291.919-1.04033.20030.03390.0880.2936-0.19850.0356-0.4185-0.20240.2496-0.02750.0845-0.03040.03090.10590.0030.070144.5902-47.758745.9411
74.16151.19150.91345.60550.5915.9784-0.05610.18740.16-0.2668-0.0460.21940.1335-0.35530.10580.09440.00460.01210.11730.00590.019733.0838-53.033738.5083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 64 )A33 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 76 )A65 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 199 )A77 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 215 )A200 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 229 )A216 - 229
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 245 )A230 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 262 )A246 - 262

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