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- PDB-5le1: VIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluoro... -

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Basic information

Entry
Database: PDB / ID: 5le1
TitleVIM-2 metallo-beta-lactamase in complex with 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid (compound 16)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / 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-6UW / FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 29, 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)29,0347
Polymers28,3531
Non-polymers6816
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-81 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.171, 60.720, 97.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-900-

HOH

21A-916-

HOH

31A-917-

HOH

41A-938-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta- ...Beta-lactamase VIM-2 / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / 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: 2-(2-chloro-6-fluorobenzyl)-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(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 344 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6UW / 2-[(2-chloranyl-6-fluoranyl-phenyl)methyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid


Mass: 319.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClFNO3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
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 2-(2-chloro-6-fluorobenzyl)-3-oxoisoindoline-4-carboxylic acid, 16 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 53782 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 14.12 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 1.065 / Net I/av σ(I): 25.7 / Net I/σ(I): 6.3 / Num. measured all: 614346
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.458.10.7652700.7780.280.8120.905100
1.45-1.5110.20.66953380.8610.2180.7050.93499.9
1.51-1.5811.50.54252950.9260.1670.5680.972100
1.58-1.6611.40.43152950.950.1340.4521.004100
1.66-1.7612.10.29553440.9780.0890.3081.039100
1.76-1.911.90.20553450.9880.0620.2141.134100
1.9-2.0912.50.13953730.9940.0410.1451.162100
2.09-2.3912.10.10453770.9950.0310.1081.181100
2.39-3.0212.30.07554690.9980.0220.0781.032100
3.02-50120.05156760.9970.0160.0541.184100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å41.02 Å
Translation6.24 Å41.02 Å

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Processing

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

4c1d


Resolution: 1.4→41.016 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 2000 3.72 %
Rwork0.1323 51699 -
obs0.1331 53699 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.55 Å2 / Biso mean: 19.9788 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.4→41.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 39 345 2103
Biso mean--19.77 35.56 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141877
X-RAY DIFFRACTIONf_angle_d0.9482565
X-RAY DIFFRACTIONf_chiral_restr0.076288
X-RAY DIFFRACTIONf_plane_restr0.007339
X-RAY DIFFRACTIONf_dihedral_angle_d17.385654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3997-1.43470.2131350.21243490362596
1.4347-1.47350.23171410.188836463787100
1.4735-1.51680.21420.164236773819100
1.5168-1.56580.16751410.155736483789100
1.5658-1.62180.16961410.138636473788100
1.6218-1.68670.16441430.133836863829100
1.6867-1.76350.14761420.122336683810100
1.7635-1.85640.1531420.123936743816100
1.8564-1.97270.1321430.128236973840100
1.9727-2.1250.14411420.123736883830100
2.125-2.33890.1611440.123137283872100
2.3389-2.67730.16341460.119737373883100
2.6773-3.37280.13831450.124637773922100
3.3728-41.0340.14461530.135539364089100
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)
12.0387-0.2069-1.28831.02540.19083.28840.00570.16570.1009-0.1053-0.00220.02550.0135-0.12070.00150.0672-0.0046-0.01180.07730.01010.0854103.826583.889212.2977
22.393-4.0957-1.86428.02311.6814.97740.18330.16510.3772-0.127-0.0305-0.0361-0.2239-0.1545-0.14220.0792-0.01360.00490.09490.01340.1259108.410491.599916.4549
30.9458-0.1187-0.5313.5310.12671.3770.0011-0.1029-0.00390.0493-0.0266-0.18020.07270.10980.01560.06130.0034-0.0150.10390.00710.0829111.641278.166724.415
44.21791.72911.77071.07391.09091.28950.2395-0.4504-0.27460.1667-0.291-0.19540.2194-0.08630.06610.15850.0052-0.00850.11320.03830.1427108.582370.703428.2001
51.6654-0.0107-0.32042.38110.47762.2483-0.04320.1034-0.0919-0.18230.03250.04080.2009-0.08850.02260.1177-0.0362-0.01060.08180.00260.0974100.868669.758916.3592
64.1583-3.7592-4.2346.79882.27525.3031-0.25630.05-0.5040.03510.0740.37860.5234-0.19330.20060.2326-0.0674-0.02090.1352-0.00430.153596.81860.62416.2731
73.03120.3130.18143.841-1.10462.9967-0.04930.31010.2242-0.14180.16120.49670.0689-0.51-0.12890.134-0.0287-0.04890.1595-0.00030.141594.030874.640411.9086
89.0118-4.7408-3.08156.56832.71955.7636-0.04810.4848-0.7288-0.3365-0.10440.38950.6593-0.08030.13640.3612-0.0802-0.03130.207-0.05010.177398.170862.24516.0115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 88 )A31 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 102 )A89 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 146 )A103 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 163 )A147 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 215 )A164 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 229 )A216 - 229
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 245 )A230 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 261 )A246 - 261

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