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- PDB-7a60: Crystal structure of VIM-2 with hydrolyzed faropenem (ring-open form) -

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Basic information

Entry
Database: PDB / ID: 7a60
TitleCrystal structure of VIM-2 with hydrolyzed faropenem (ring-open form)
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / antibiotic / faropenem / catalysis
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 / Chem-QZH / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: 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
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,57014
Polymers51,3872
Non-polymers1,18312
Water6,918384
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2857
Polymers25,6931
Non-polymers5926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2857
Polymers25,6931
Non-polymers5926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.179, 79.380, 67.332
Angle α, β, γ (deg.)90.000, 130.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-546-

HOH

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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) / Variant (production host): pLysS / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / 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-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.: 2 / Source method: obtained synthetically / Formula: C12H17NO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
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: 0.88 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.47→51.34 Å / Num. obs: 68197 / % possible obs: 98.1 % / Redundancy: 7 % / CC1/2: 0.991 / Rpim(I) all: 0.039 / Net I/σ(I): 9.2
Reflection shellResolution: 1.47→1.5 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3241 / CC1/2: 0.469 / Rpim(I) all: 0.699

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz3

4bz3


Resolution: 1.47→51.34 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 3296 4.84 %
Rwork0.1626 64800 -
obs0.1638 68096 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.7 Å2 / Biso mean: 27.7928 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.47→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 88 384 3958
Biso mean--31.29 36.13 -
Num. residues----462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.490.32261520.29272527267994
1.49-1.510.28961190.27212659277897
1.51-1.540.29351410.28242656279796
1.54-1.560.27611600.24572631279197
1.56-1.590.27161490.24212669281897
1.59-1.620.25381490.22162654280397
1.62-1.650.26531620.2172640280297
1.65-1.680.24831520.20562673282597
1.68-1.720.19361680.19672627279598
1.72-1.760.23481020.18262735283798
1.76-1.80.21511810.17592651283298
1.8-1.850.22661270.1652717284498
1.85-1.910.19541180.17112704282298
1.91-1.970.20441180.17692705282398
1.97-2.040.17921210.15022747286898
2.04-2.120.17511230.14842715283899
2.12-2.220.18191050.13842742284798
2.22-2.330.168990.15112787288699
2.33-2.480.1735980.14482760285899
2.48-2.670.18781160.14812757287399
2.67-2.940.17271730.14852734290799
2.94-3.360.18361510.148227422893100
3.37-4.240.14331470.134827622909100
4.24-51.340.17991650.166128062971100
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)
10.59450.144-1.47313.61791.6185.9015-0.1825-1.1381-1.02491.04410.80760.69910.63830.2064-0.48660.43260.0774-0.13880.44720.20420.5214-13.9580.70567.758
26.14710.7402-4.42245.1409-1.15046.80240.2678-0.2363-0.41580.0975-0.1261-0.16960.34040.0171-0.03680.2071-0.0263-0.10730.13180.02150.1912-13.13974.77662.0113
32.2487-1.0765-0.83572.2516-0.34695.02250.1234-0.17130.0376-0.0462-0.0212-0.21510.05580.0254-0.05650.1159-0.0164-0.04960.0954-0.00580.1755-11.870210.61857.8586
43.82790.26811.50252.06360.62163.24820.0659-0.23440.02640.1709-0.0494-0.1442-0.0709-0.1070.01020.1423-0.0158-0.01320.0843-0.0160.1352-16.823717.278758.1784
51.3024-0.97510.33665.80624.53094.6714-0.0926-0.03140.0279-0.5809-0.0360.0786-0.3112-0.16010.12770.2171-0.0028-0.03110.15650.00960.1515-22.26318.787246.7585
62.54390.3330.28863.2491-0.01241.94740.05630.137-0.1398-0.2993-0.0458-0.11140.03310.0211-0.01310.13680.00940.00120.0873-0.02360.1114-18.85043.189946.9088
72.63042.62590.56326.01221.0161.35240.043-0.0404-0.09050.05-0.15010.22250.1423-0.14130.13740.16570.0046-0.05880.15990.01250.1487-26.3944-2.075349.1506
83.1961-1.7167-1.9373.53321.83484.1470.1543-0.44310.5705-0.21170.4978-1.307-0.56311.2912-0.52470.2794-0.1047-0.03910.4413-0.16440.5425-24.1767-4.06379.5419
93.73021.3311-1.12224.1859-1.43625.45280.0629-0.21950.13820.2184-0.0308-0.1444-0.02010.36740.00240.09730.0233-0.05040.1397-0.00280.1396-31.4889-12.339181.6774
103.57290.0111.79495.82471.12446.92770.24640.09810.05380.38170.0002-0.76680.07940.7853-0.10120.16430.0297-0.07190.26850.02970.3116-23.0313-16.685283.3829
113.4493-0.11961.1863.0329-0.54363.12290.02470.1033-0.2212-0.0933-0.0008-0.19060.3670.2021-0.04180.16230.05960.0070.11290.00220.1444-35.811-22.993974.2918
121.4333-0.07820.47592.6169-0.56422.1286-0.0222-0.04670.07270.03860.0160.1514-0.0557-0.06720.00230.08540.0101-0.00660.1137-0.00320.1315-45.174-11.180575.6779
132.3431-1.56150.19975.4779-2.68743.970.07140.22290.151-0.17960.00570.1655-0.1547-0.1886-0.18810.09-0.0238-0.04470.13280.01750.1961-44.0426-2.576668.9923
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 145 )A89 - 145
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 163 )A146 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 245 )A164 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 263 )A246 - 263
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 44 )B32 - 44
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 88 )B45 - 88
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 102 )B89 - 102
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 146 )B103 - 146
12X-RAY DIFFRACTION12chain 'B' and (resid 147 through 245 )B147 - 245
13X-RAY DIFFRACTION13chain 'B' and (resid 246 through 263 )B246 - 263

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