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- PDB-7a5z: Structure of VIM-2 metallo-beta-lactamase with hydrolysed Faropen... -

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Basic information

Entry
Database: PDB / ID: 7a5z
TitleStructure of VIM-2 metallo-beta-lactamase with hydrolysed Faropenem imine product
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / VIM-2 / faropenem / antimicrobial resistance / penems / carbapenems
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
Chem-QZH / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.29 Å
AuthorsLucic, A. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Faropenem reacts with serine and metallo-beta-lactamases to give multiple products.
Authors: Lucic, A. / Hinchliffe, P. / Malla, T.R. / Tooke, C.L. / Brem, J. / Calvopina, K. / Lohans, C.T. / Rabe, P. / McDonough, M.A. / Armistead, T. / Orville, A.M. / Spencer, J. / Schofield, C.J.
History
DepositionAug 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3119
Polymers25,6931
Non-polymers6188
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-68 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.647, 74.680, 78.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

21A-560-

HOH

31A-576-

HOH

41A-580-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 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: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / Variant (production host): DE3 / References: UniProt: Q9K2N0

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Non-polymers , 6 types, 198 molecules

#2: Chemical ChemComp-QZH / (5~{Z})-2-[1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-(4-oxidanylbutylidene)-2~{H}-1,3-thiazole-4-carboxylic acid


Mass: 303.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Magnesium Chloride, 35% PEG 8000, Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.29→49.97 Å / Num. obs: 48222 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.991 / Rpim(I) all: 0.032 / Net I/σ(I): 13.8
Reflection shellResolution: 1.29→1.31 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2353 / CC1/2: 0.629

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.48 Å54.2 Å
Translation1.48 Å54.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
xia2data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.29→48.88 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1583 2411 5 %RANDOM
Rwork0.1401 45808 --
obs0.141 48219 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.53 Å2 / Biso mean: 20.6118 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.29→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 40 200 1961
Biso mean--17.13 31.92 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.29-1.320.2751330.26742647278099
1.32-1.340.23661400.246526592799100
1.34-1.380.24941560.228426502806100
1.38-1.410.24251370.216426592796100
1.41-1.450.18551280.195326592787100
1.45-1.490.20421280.182226812809100
1.49-1.540.17181390.173227152854100
1.54-1.590.18741520.163626452797100
1.59-1.660.17531620.148926742836100
1.66-1.730.16371360.137126482784100
1.73-1.820.14771380.126427262864100
1.83-1.940.13841310.119726972828100
1.94-2.090.12281460.112926922838100
2.09-2.30.14081340.112627122846100
2.3-2.630.14891320.113927592891100
2.63-3.320.14491640.127527232887100
3.32-48.880.14971550.136928623017100
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)
12.246-0.71090.73251.85170.01014.1719-0.2182-0.36630.34730.25460.14510.0221-0.4124-0.38360.02740.26610.02390.00380.1893-0.04550.1609-23.7719-3.8606-2.2644
23.66-0.1041-1.24541.62250.59243.17410.0182-0.18370.08450.09820.0970.0175-0.08930.1236-0.11880.18050.00540.00460.0971-0.01440.0799-19.2484-7.9943-6.8188
33.8542-0.4965-1.51941.09240.53932.86220.03620.0390.1975-0.03410.0676-0.0561-0.09470.1278-0.07750.1491-0.010.01070.0682-0.01080.0741-16.8406-10.3612-12.7599
44.22561.9472-0.1583.289-0.10550.57740.0908-0.110.40910.0270.0066-0.0172-0.32610.0741-0.06990.2184-0.01030.03640.0831-0.00860.1317-19.6963-0.9004-14.8703
51.3019-0.0351-0.24911.5073-0.15411.48210.0270.071-0.0659-0.09080.01280.01360.02580.0507-0.01840.14040.0079-0.00020.0937-0.01560.0576-17.3112-20.4902-19.2541
60.96-0.0905-0.18731.4641-0.26121.73540.0208-0.1397-0.06470.15210.03650.05030.04220.0594-0.04750.16680.0111-0.01010.12450.00520.0706-17.1376-21.041-4.4388
74.637-0.2511-0.11952.7201-0.5882.37450.035-0.1766-0.38880.1910.0153-0.1730.51490.4329-0.0250.24560.0857-0.0340.17630.00650.1169-13.1647-31.3618-4.0419
82.2331-0.69070.50281.9036-0.32560.75890.0037-0.08550.09260.2438-0.0298-0.2032-0.1050.47440.02320.1722-0.0113-0.03450.25630.00610.0726-10.8463-17.407-1.87
96.18192.2389-0.70274.4984-0.72283.7157-0.0674-0.2166-0.39270.07790.046-0.01560.40030.011-0.00540.25560.0228-0.01580.14540.0310.1001-19.0996-28.17013.9468
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 102 )A89 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 183 )A103 - 183
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 215 )A184 - 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 263 )A246 - 263

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