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- PDB-6zyn: Structure of VIM-2 with 2-Mercaptomethyl-thiazolidine L-anti-1b -

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Basic information

Entry
Database: PDB / ID: 6zyn
TitleStructure of VIM-2 with 2-Mercaptomethyl-thiazolidine L-anti-1b
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / lactamase / zinc / inhibitor
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
FORMIC ACID / Chem-QT2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.40001375561 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: Chem Sci / Year: 2021
Title: 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
Authors: Rossi, M.A. / Martinez, V. / Hinchliffe, P. / Mojica, M.F. / Castillo, V. / Moreno, D.M. / Smith, R. / Spellberg, B. / Drusano, G.L. / Banchio, C. / Bonomo, R.A. / Spencer, J. / Vila, A.J. / Mahler, G.
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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)52,52214
Polymers51,3872
Non-polymers1,13512
Water8,845491
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2617
Polymers25,6931
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2617
Polymers25,6931
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.480, 79.170, 78.070
Angle α, β, γ (deg.)90.000, 90.495, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QT2 / (2~{S},4~{R})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 279.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91588 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91588 Å / Relative weight: 1
ReflectionResolution: 1.4→55.59 Å / Num. obs: 80433 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.986 / Rpim(I) all: 0.077 / Net I/σ(I): 4.8
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4109 / CC1/2: 0.567 / Rpim(I) all: 0.357

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.40001375561→55.587604555 Å / Cross valid method: FREE R-VALUE / σ(F): 71.9010155309 / Phase error: 20.8072397251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176227683252 3908 4.87385106569 %
Rwork0.149734464045 76275 -
obs0.154298105135 80183 99.4073963873 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1785883793 Å2
Refinement stepCycle: LAST / Resolution: 1.40001375561→55.587604555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 52 491 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331517685953798
X-RAY DIFFRACTIONf_angle_d1.248353060455233
X-RAY DIFFRACTIONf_chiral_restr0.10275642905591
X-RAY DIFFRACTIONf_plane_restr0.0077213187091694
X-RAY DIFFRACTIONf_dihedral_angle_d15.42130563061345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4003-1.42440.2657887591112130.2570085054543758X-RAY DIFFRACTION93.6456516322
1.4244-1.45030.2378877898771870.2447794735273773X-RAY DIFFRACTION94.0897755611
1.4503-1.47820.2848461081932240.2441069077083752X-RAY DIFFRACTION93.4030370924
1.4782-1.50830.2586787217531810.2321531087043788X-RAY DIFFRACTION93.9717191764
1.5083-1.54110.2409516473071960.2136144195693752X-RAY DIFFRACTION94.0350877193
1.5411-1.57690.2322252500772130.2019502639333809X-RAY DIFFRACTION94.1889218595
1.5769-1.61630.2233945583971640.1955072030243774X-RAY DIFFRACTION94.9195171026
1.6163-1.660.1957345815422140.1892172344893797X-RAY DIFFRACTION94.1482767171
1.66-1.70880.191711240331680.1800122228643812X-RAY DIFFRACTION95.2523738131
1.7088-1.76390.1878105117941720.1673532513853848X-RAY DIFFRACTION95.3183056725
1.7639-1.82680.1666430014781650.1691581254513826X-RAY DIFFRACTION95.3639082752
1.8268-1.89980.176523491951770.1611140772383796X-RAY DIFFRACTION94.9237309327
1.8998-1.98610.1725876110622150.1606051358473819X-RAY DIFFRACTION94.3661971831
1.9861-2.09060.1622255592072020.1442107841083815X-RAY DIFFRACTION94.7590660705
2.0906-2.22130.1826077209881690.1398772917213838X-RAY DIFFRACTION95.5677290837
2.2213-2.39220.1638470927342260.1379605638353794X-RAY DIFFRACTION94.2140551279
2.3922-2.6320.179724829932110.1291786078953818X-RAY DIFFRACTION94.5986124876
2.632-3.01050.1721518642191770.1293479298163854X-RAY DIFFRACTION95.2310353348
3.0105-3.78410.1408874386721850.1222563402233872X-RAY DIFFRACTION95.2053110401
3.7841-15.71610.1626687359351970.1293643243413919X-RAY DIFFRACTION95.1675570665
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)
16.806386380460.8453496626-1.3383838371.610085235730.0503769340212.482405216820.0457401259867-0.583035011543-0.4268981745140.527324094070.335108298760.8623137692120.51357753137-0.472017540735-0.25672047850.452191317389-0.07183064301250.05108663255160.1660204447290.13404331060.3172067673826.014796806865.83183644047111.240895417
24.893106238981.533396307230.3594063953174.06447590114-0.03692054967211.95732382177-0.0212827740685-0.152348217572-0.1129706322140.1565007914560.0221515303059-0.1097264378550.191052235092-0.03690909872590.01020102874290.1561646014220.001253131867170.02139606050440.0292899937143-0.005274172209690.072207126032912.761409295413.1859165715107.276328848
33.78518244863-2.862275343413.527219438965.66008221876-2.896000375883.29706073367-0.0760229130237-0.376647936881-0.0458313626730.5961000744340.1278146631830.1154601836790.131803384503-0.285076986527-0.01025874850680.1975597625540.001927381640670.03012799039220.110416769965-0.02185821451150.09043903497168.8889649928918.9995164114.061533249
41.21588045937-0.01335665076480.587051158371.818986181010.822256125382.800237302070.0168314483236-0.01827215817420.1021163284350.0280597967512-0.0269903130355-0.0191881767206-0.0598222457026-0.0446286631990.03010675664330.09115795659560.00157755162940.02529287497580.0291276258941-0.006038434024790.11462120455911.73698229123.658284031598.6666366439
50.7928294647-0.6399158406620.191445545112.155276249990.3070091662151.081198529410.02464688423920.008143769264250.0728137246725-0.09399161153510.042827900381-0.246507122275-0.03874482814040.0961709577721-0.04637371969090.0908046527043-0.01423554968370.02673286602820.0472665783205-0.005231446292230.12267328498720.393284029217.265061349694.3500160491
60.473636349877-0.6435911522890.2689356648363.92883458001-3.897398885864.33930455120.04152878402740.162676787562-0.162070837508-0.07482460970540.1371883806660.4638259717280.0999150797197-0.386540353906-0.1980911429950.202589513512-0.02166929290570.008102527310830.0454933408529-0.0214503762210.171831091678.437500933383.5839816522191.8308077386
76.422145364821.041702385135.105719694192.693535986270.7943454296395.588425149170.2160375229410.543861311715-0.0742436219216-0.227747335742-0.00476300702772-0.3120231071530.3007462580640.507408412804-0.1889045186970.1572083360210.02702564809210.05784269220170.0492285279267-0.02258511124450.13802663219121.50498763666.4571762775986.2617758945
82.98368561659-0.188263205418-0.2540484590521.264914306760.3566417117242.06102025771-0.0797812579099-0.184303598481-0.1928970338830.1825084529850.0529709826314-0.2077249314440.2408830311750.1132983633150.025262011750.128153446590.0119934114865-0.0121636405930.0383831831985-0.0003147615227060.13865626486820.66318079634.24275238535101.09538749
92.552660390452.231933636812.421695959192.496627688121.960573436135.108380757070.02166649827150.0155755240626-0.0575249745912-0.0214848722139-0.00342930823448-0.0973155784170.124168506614-0.0757798216069-0.01702788303080.1491104164490.01881974922180.02825233624120.0311678327829-0.006101126541890.12005092123313.6871099384-0.99237402938287.7049671737
104.684579391441.16183421965-0.3568196127243.135740382040.3515864075231.70008221170.0580826736074-0.2857707793910.2152197162830.322032445299-0.0167973368923-0.0157382023242-0.3029049758550.082425343814-0.02607108720420.215900833428-0.00210887750834-0.003947023847350.0546231640894-0.002278838300620.0788662613029-13.9334692914-5.05603765912107.916676208
111.95446064460.297723733107-0.968617983672.00220979432-0.5292534230813.823067660240.0193029639102-0.161065693142-0.04664003160240.319189975328-0.0256303466644-0.0399372599374-0.10245567980.09212688287870.02486702906740.133841874590.01105957834470.004844607085360.01935350898280.01046798566460.0998037392267-13.2380294702-13.1675630534107.123469369
121.76288147141-0.06582169792850.182341396512.4660503909-0.65850577692.29110295805-0.01965705600570.0460395419756-0.143706732826-0.0478299347336-0.030583993387-0.2153380305960.2264099333810.1327543982630.03546188687460.1195699097560.02369779044930.02522978970190.03270221455490.001757123910320.151885706152-11.5978006766-20.234456568796.5173330376
131.2528350761-1.333217235180.6268985399012.80089238271-1.976102962321.716363837270.0444943573279-0.00127880553618-0.164965260939-0.1445159161680.09295069366430.09056975766680.194290416704-0.0452186778517-0.1546485499240.1297256858550.002747444656050.01146665868470.0506954224158-0.0214427785940.0919792183501-18.3795360113-18.460038775291.4445988212
140.9605338806530.137081772101-0.4322843616091.50186245337-0.3276515192251.867513009390.02426622473670.003571566893950.02761405772550.0296881291020.02564405578610.138003510077-0.00803240957132-0.116344033283-0.04315266509970.0816166902273-0.0002349055372850.01774927801710.04014840959740.002525154557540.102752840305-23.117119878-8.7691522765294.8977296195
150.114580093172-0.466365131432-0.3878919561335.184737600884.921248772054.760768823040.02474277993330.07857499988290.104800427576-0.0222057218620.176911280929-0.402348766252-0.1813447530160.44512335093-0.2068788031810.151625420391-0.02026791239370.03137485056590.09180608459830.009228628877140.157021177119-10.31475969582.3769632248391.1192388018
164.523690777142.77439886884-4.695587624183.39797627832-1.576264996155.851744759790.06599307557770.5197484079630.0824791151374-0.0184641777540.05123603379110.183745308009-0.272788776954-0.434629007836-0.06410201089680.1322178952380.0184443503745-0.0181445128880.03730339324910.01126149785350.102340341183-22.8613482913-1.4086045054485.166386297
171.981970681150.7873000190720.6894694788291.145740199340.3425219719431.498070287290.015752839013-0.07436850593050.2362158414690.140645719046-0.006442492478830.157927492155-0.191514956359-0.1130201181160.01432082580130.1340058319530.01222625783630.04242577994840.05072991432180.007352219119540.130825736125-23.26022482341.2888726058699.9090122859
183.373857684151.31946289908-1.605460051713.94444778275-0.6112820069695.21926546181-0.02423599813260.08236171191380.05154245419590.0486892789190.0634570691350.0749930950116-0.2302066338440.149268608969-0.05683945574770.136822338826-0.00142943284734-0.01329810434750.01979885849430.0160696318370.112199120312-16.04857730196.6559991971387.4866594813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 146 )
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 199 )
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 215 )
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 245 )
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 262 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 122 )
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 146 )
13X-RAY DIFFRACTION13chain 'B' and (resid 147 through 163 )
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 199 )
15X-RAY DIFFRACTION15chain 'B' and (resid 200 through 215 )
16X-RAY DIFFRACTION16chain 'B' and (resid 216 through 229 )
17X-RAY DIFFRACTION17chain 'B' and (resid 230 through 245 )
18X-RAY DIFFRACTION18chain 'B' and (resid 246 through 262 )

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