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- PDB-6y6j: VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products -

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Basic information

Entry
Database: PDB / ID: 6y6j
TitleVIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products
ComponentsMetallo-beta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / Metallo beta lactamases / VIM2 / biapenem / enzyme product complex
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
Biapenem Imine hydrolysis product / Biapenem Enamine hydrolysis product / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLucic, A. / Schofield, C.J. / Brem, J. / McDonough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Structure of metallo-beta-lactamase VIM-2 in complex with the imine and enamine form of hydrolysed Biapenem
Authors: Lucic, A. / Saward, B.G. / Brem, J. / McDonough, M.A. / Calvopina, K. / Schofield, C.J.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)25,8089
Polymers24,7671
Non-polymers1,0418
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-61 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.324, 74.020, 78.354
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-906-

HOH

21A-937-

HOH

31A-993-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase VIM-2


Mass: 24766.518 Da / Num. of mol.: 1 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-2 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Lemo21 pLySs / References: UniProt: D1MEN9

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Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-OEN / Biapenem Imine hydrolysis product


Mass: 369.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OEQ / Biapenem Enamine hydrolysis product / (2~{S},3~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[[(6~{R})-6,7-dihydro-5~{H}-pyrazolo[1,2 -a][1,2,4]triazol-4-ium-6-yl]sulfanyl]-3-methyl-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid


Mass: 369.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.82 Å3/Da / Density % sol: 32.29 %
Description: 100 x 20 x 10 micrometer crystal, rhomboid shape crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% w/v PEG 8000, 0.2M magnesium chloride, 0.1M TRIS pH 7.0

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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 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.5→27.61 Å / Num. obs: 30180 / % possible obs: 99.56 % / Redundancy: 13.3 % / Biso Wilson estimate: 13.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.03 / Rrim(I) all: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.35 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 2951 / CC1/2: 0.975 / Rpim(I) all: 0.095 / Rrim(I) all: 0.337 / % possible all: 98.96

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.07 Å27.61 Å
Translation5.07 Å27.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.5→27.61 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1573 1406 4.66 %
Rwork0.1287 28772 -
obs0.1302 30179 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.74 Å2 / Biso mean: 19.0799 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: final / Resolution: 1.5→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 56 200 1983
Biso mean--16.07 31.2 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.550.18331350.13912816295199
1.55-1.620.16071390.13022830296999
1.62-1.690.15711430.12232835297899
1.69-1.780.13951420.12522820296299
1.78-1.890.14841320.124228652997100
1.89-2.040.1571440.119328653009100
2.04-2.240.14781410.123228893030100
2.24-2.560.14161390.124328843023100
2.56-3.230.15631410.133229263067100
3.23-27.610.17111500.134730423192100
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)
16.0843-0.62562.1830.74520.3645.6037-0.1804-0.38030.57890.28930.1126-0.1885-0.481-0.17910.1480.26160.0121-0.01050.1241-0.05570.1586-23.6147-3.7744-2.3801
28.29470.0763-0.52892.22431.27373.5862-0.0047-0.26160.15640.11380.0946-0.0762-0.09720.1966-0.09630.18820.0085-0.00280.0761-0.01370.0622-18.4824-7.7692-6.7821
38.89280.2564-3.5071.13250.18183.37050.0803-0.02060.1952-0.03110.0388-0.0312-0.07730.1645-0.11980.1498-0.00790.00560.0393-0.01470.0577-16.5366-10.2382-12.7464
47.58083.9718-0.01558.0273-0.53731.29740.0673-0.16070.48580.1130.0344-0.181-0.34680.0881-0.04480.22910.00450.03880.0606-0.00640.1312-20.0901-1.4472-15.3027
51.78090.1066-0.22961.4132-0.19861.57790.0330.0441-0.0874-0.08280.0104-0.01040.03580.0836-0.04020.13040.0102-0.00010.062-0.01840.056-16.0065-19.912-17.3303
60.81412.16662.39647.65588.27898.9686-0.0172-0.3091-0.04750.1564-0.38770.57390.0372-0.65810.42910.2372-0.0106-0.00230.15980.0210.1299-24.2658-23.1986-0.6727
77.78592.60521.79353.98090.11641.95860.20270.0637-0.64950.2115-0.0869-0.25880.47320.4179-0.10930.25870.0936-0.0210.1660.02590.1193-12.8661-30.9865-3.5796
84.745-2.2528-0.62813.0045-0.17150.57070.003-0.16950.21260.3471-0.0426-0.3323-0.24160.62860.0650.1801-0.0411-0.04460.27680.02220.0807-10.7913-16.9072-1.8608
98.81613.62920.75127.29350.08046.905-0.0294-0.3307-0.44150.09820.0010.05830.3412-0.07590.01490.23340.029-0.02130.10620.02260.0837-18.8094-27.63074.1954
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 199 )A103 - 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 263 )A246 - 263

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