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- PDB-8r5u: VIM-2 metallo-beta-lactamase in complex with benzebisheterocycle ... -

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Basic information

Entry
Database: PDB / ID: 8r5u
TitleVIM-2 metallo-beta-lactamase in complex with benzebisheterocycle compound 14
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / inhibitor
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
FORMIC ACID / : / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes.
Authors: Villamil, V. / Rossi, M.A. / Mojica, M.F. / Hinchliffe, P. / Martinez, V. / Castillo, V. / Saiz, C. / Banchio, C. / Macias, M.A. / Spencer, J. / Bonomo, R.A. / Vila, A. / Moreno, D.M. / Mahler, G.
History
DepositionNov 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,45815
Polymers51,3872
Non-polymers1,07113
Water7,170398
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2528
Polymers25,6931
Non-polymers5597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2067
Polymers25,6931
Non-polymers5136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.636, 79.375, 67.585
Angle α, β, γ (deg.)90.000, 130.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 25693.488 Da / Num. of mol.: 2
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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-Y4E / [(1~{R},3~{a}~{R})-1,3,3~{a},4-tetrahydro-[1,3]thiazolo[3,4-a]benzimidazol-1-yl]methanethiol


Mass: 224.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 28% PEG3350, 0.1M Mg(HCO2)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.56→33.79 Å / Num. obs: 58649 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rpim(I) all: 0.066 / Net I/σ(I): 6.7
Reflection shellResolution: 1.56→1.59 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2895 / CC1/2: 0.466 / Rpim(I) all: 0.829

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→33.789 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 2816 4.8 %
Rwork0.1613 55796 -
obs0.1631 58612 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.25 Å2 / Biso mean: 26.2711 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: final / Resolution: 1.56→33.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 79 398 3969
Biso mean--28.65 36.72 -
Num. residues----463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.56-1.58690.34681300.31022793
1.5869-1.61580.30591130.28422784
1.6158-1.64680.30681180.2662781
1.6468-1.68050.26091260.25232811
1.6805-1.7170.28711400.22422777
1.717-1.75690.24741470.20952759
1.7569-1.80090.21821600.20242792
1.8009-1.84960.23021300.19022779
1.8496-1.9040.24621430.17382772
1.904-1.96540.21141640.16832789
1.9654-2.03570.20011340.14392780
2.0357-2.11720.18761220.14152789
2.1172-2.21350.17361430.13862770
2.2135-2.33020.17131260.14412837
2.3302-2.47610.17132030.14222722
2.4761-2.66720.18741470.14522770
2.6672-2.93550.1691330.14582818
2.9355-3.35990.2051320.14122806
3.3599-4.23190.16831520.12992806
4.2319-33.7890.19421530.16012861
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)
13.578-1.5368-2.17567.70253.92976.9833-0.3588-1.0602-0.96391.02810.49160.34360.68170.4159-0.11930.30950.0617-0.06110.33680.15380.3398-14.39910.780968.0131
27.39431.9909-4.50244.0391-1.13385.52120.0856-0.0611-0.14380.10360.0249-0.18460.29930.0661-0.04730.22260.0065-0.060.129-0.00130.1706-12.93414.892562.1062
33.9016-0.7073-1.16641.7225-0.18573.9150.1183-0.2762-0.02320.018-0.0267-0.2043-0.00470.179-0.07680.1257-0.0121-0.03020.0764-0.00740.1301-12.089910.757258.1852
45.6752-0.05392.00481.77920.78963.08840.1114-0.3501-0.07450.11020.0079-0.13170.1203-0.0262-0.10110.1855-0.02210.0050.0857-0.01180.137-14.098814.633761.3169
51.58820.37940.40651.89560.55751.3472-0.02940.06980.0446-0.29710.0196-0.0545-0.21370.02330.00460.1999-0.01520.01430.07830.00960.1038-18.79914.937348.464
65.3421-3.96482.37644.8902-2.7921.6001-0.073-0.2963-0.20220.19990.09580.26830.1904-0.2613-0.04170.2451-0.0263-0.0070.0962-0.01740.1577-27.3868-1.455653.3294
78.94132.2015-1.85864.1172-0.04193.0604-0.10210.6046-0.4011-0.36780.0711-0.0245-0.00310.06740.07210.2261-0.0096-0.00780.106-0.0340.1113-23.12580.97739.6139
82.75740.348-1.34941.2023-0.50863.96370.1009-0.1052-0.2097-0.0053-0.0057-0.19130.19210.29860.03460.21460.01490.00520.1021-0.02120.1743-12.5776-0.788350.0828
96.29172.82230.2232.0022-0.95971.9515-0.1609-0.0609-0.1199-0.13390.0961-0.05940.2105-0.02910.02690.21830.0005-0.00620.0691-0.02310.145-27.2269-6.249846.7417
102.9608-0.4507-1.4635.56671.81113.1469-0.3855-0.39910.8425-0.00830.0872-0.8284-0.88671.3581-0.06980.3672-0.1597-0.17890.46140.06160.4326-24.2584-4.506979.4481
113.24581.0025-1.31073.6448-1.11765.338-0.0458-0.10640.11530.1785-0.0526-0.1235-0.14890.18770.10620.13590.0059-0.04590.09680.01830.1411-31.6264-12.678681.7545
124.02740.95030.75785.963.58688.01460.02260.11640.25670.3690.0678-0.42720.09210.7008-0.08670.18150.0166-0.05140.22160.07720.2476-23.2194-17.200283.3381
132.9821-0.61682.28692.2782-0.92884.2491-0.0948-0.0670.0310.0535-0.0908-0.2190.03410.05490.16590.19720.03050.01360.07950.01940.163-34.6539-19.656377.9637
143.6766-0.56521.33022.4902-0.7053.97340.08990.1476-0.2051-0.2846-0.0666-0.08110.41820.185-0.01320.24070.02750.03170.063-0.00380.141-37.1993-25.996772.2687
151.2081-0.43370.42272.3401-0.5241.6734-0.012-0.1083-0.09440.08570.0290.12520.0277-0.0834-0.00580.1513-0.00340.01350.08920.01230.1215-45.6012-17.255177.8855
162.65193.87723.09276.10364.12855.6159-0.05310.2344-0.0031-0.25450.1335-0.2094-0.20350.2832-0.17990.18410.0234-0.01430.1154-0.00050.1749-39.9503-3.036467.8818
174.24971.009-0.34994.109-3.0482.3169-0.1025-0.06720.14660.12240.11240.358-0.3239-0.27-0.0380.16520.02740.00630.08450.00490.1535-53.1962-6.75572.677
187.55220.3801-3.16960.7397-0.43282.63180.0285-0.3440.23390.2621-0.0393-0.0225-0.32250.07410.00970.26140.0225-0.02020.1009-0.00750.1509-42.0492-4.514982.428
194.7583-0.78650.5674.8151-0.85642.02840.00060.12020.1650.10650.00110.1488-0.1650.0501-0.07080.16040.0053-0.00750.05810.01250.1416-46.79451.525468.2356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 44 )A32 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 64 )A45 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 88 )A65 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 122 )A89 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 199 )A123 - 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 262 )A246 - 262
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 44 )B32 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 88 )B45 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 102 )B89 - 102
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 122 )B103 - 122
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 146 )B123 - 146
15X-RAY DIFFRACTION15chain 'B' and (resid 147 through 199 )B147 - 199
16X-RAY DIFFRACTION16chain 'B' and (resid 200 through 215 )B200 - 215
17X-RAY DIFFRACTION17chain 'B' and (resid 216 through 229 )B216 - 229
18X-RAY DIFFRACTION18chain 'B' and (resid 230 through 245 )B230 - 245
19X-RAY DIFFRACTION19chain 'B' and (resid 246 through 263 )B246 - 263

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