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- PDB-6zys: Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b -

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Basic information

Entry
Database: PDB / ID: 6zys
TitleStructure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b
ComponentsBeta-lactamase IMP-1
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / lactamase / zinc / inhibitor
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-QST / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8700095823 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 IMP-1
B: Beta-lactamase IMP-1
C: Beta-lactamase IMP-1
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03019
Polymers101,2034
Non-polymers1,82715
Water8,863492
1
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7114
Polymers25,3011
Non-polymers4103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8356
Polymers25,3011
Non-polymers5345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7735
Polymers25,3011
Non-polymers4724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7114
Polymers25,3011
Non-polymers4103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.7824, 77.9686, 261.906
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Beta-lactamase IMP-1 / BLAIMP / Beta-lactamase type II / Penicillinase / Class B1 Metallo-beta-lactamase IMP-1


Mass: 25300.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P52699, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-QST / (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 279.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1 ul reagent.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→58.153 Å / Num. obs: 83944 / % possible obs: 100 % / Redundancy: 26.2 % / Biso Wilson estimate: 28.727022947 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 18.6
Reflection shellResolution: 1.87→1.91 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4532 / CC1/2: 0.784 / Rpim(I) all: 0.469

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HH4
Resolution: 1.8700095823→58.1529684507 Å / SU ML: 0.197803143802 / Cross valid method: FREE R-VALUE / σ(F): 1.32910924106 / Phase error: 21.2790522281
RfactorNum. reflection% reflection
Rfree0.201348319116 4049 4.83508872489 %
Rwork0.174089105023 79693 -
obs0.175417928252 83742 99.8795367532 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.0579551912 Å2
Refinement stepCycle: LAST / Resolution: 1.8700095823→58.1529684507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6863 0 88 492 7443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116213175177125
X-RAY DIFFRACTIONf_angle_d1.320616083099678
X-RAY DIFFRACTIONf_chiral_restr0.08837313456381072
X-RAY DIFFRACTIONf_plane_restr0.01458938010331206
X-RAY DIFFRACTIONf_dihedral_angle_d14.46925038472565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.871-1.8920.3208860127561320.2827849106042680X-RAY DIFFRACTION99.7516849947
1.892-1.91510.2971887920481210.2694134290222718X-RAY DIFFRACTION99.7891036907
1.9151-1.93930.266338593431330.2519044673792708X-RAY DIFFRACTION99.8594024605
1.9393-1.96480.259476092941210.2284092001772745X-RAY DIFFRACTION99.791086351
1.9648-1.99180.2798334488681400.222658370632697X-RAY DIFFRACTION99.8240675581
1.9918-2.02020.2297874783841290.2043932167612709X-RAY DIFFRACTION99.8241294407
2.0202-2.05040.2348607796961600.2049629253242719X-RAY DIFFRACTION99.8959056211
2.0504-2.08240.1973866183921200.2051923754342696X-RAY DIFFRACTION99.8581560284
2.0824-2.11660.2150424725431390.1979544236622764X-RAY DIFFRACTION99.8280605227
2.1166-2.15310.2428022621431420.1961630644522680X-RAY DIFFRACTION99.8231340644
2.1531-2.19220.2107293525681570.2002335416232710X-RAY DIFFRACTION99.9302892994
2.1922-2.23440.2245518295091320.1942512963812739X-RAY DIFFRACTION99.826147427
2.2344-2.280.2298506312111440.1883809527242660X-RAY DIFFRACTION99.7864768683
2.28-2.32960.1990880731821490.1886232267022745X-RAY DIFFRACTION99.7931034483
2.3296-2.38380.2073390926891410.1867729439022695X-RAY DIFFRACTION99.9295278365
2.3838-2.44340.2209924932911470.1816878453552777X-RAY DIFFRACTION99.795221843
2.4434-2.50940.2698597644581140.1854386321732716X-RAY DIFFRACTION99.8941051888
2.5094-2.58330.2010118846621260.1852741744552769X-RAY DIFFRACTION100
2.5833-2.66670.2276919574841210.1777696668112742X-RAY DIFFRACTION100
2.6667-2.7620.2152651633051440.1760329748872750X-RAY DIFFRACTION99.9309392265
2.762-2.87250.2138537960341460.181184410512779X-RAY DIFFRACTION99.96582365
2.8725-3.00330.215933695811550.1834822171782718X-RAY DIFFRACTION100
3.0033-3.16160.1981401760181330.1763688005192753X-RAY DIFFRACTION100
3.1616-3.35970.1791195429411500.1685093502792763X-RAY DIFFRACTION100
3.3597-3.6190.1924970362911370.1615057007442790X-RAY DIFFRACTION100
3.619-3.98320.2010853347441730.1631132846412794X-RAY DIFFRACTION100
3.9832-4.55930.1601617066531350.1418704989142819X-RAY DIFFRACTION100
4.5593-5.74350.1720015821841470.1478331135222860X-RAY DIFFRACTION100
5.7435-58.1520.178383284311610.1543893219892998X-RAY DIFFRACTION99.4647355164
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.97436740338-0.294187154599-1.21547699023.877923323831.439599935354.86183484624-0.146878769024-0.7196757242720.2156284699620.7524416089270.313273479076-0.2110658976730.1581197936550.26891857015-0.1335471310710.4043059336570.0259274577345-0.06325943094270.2667887346760.03543699595780.18791418290765.583500337165.239033479304.355023091
22.828446296370.108046580646-0.3685202017882.859181352961.364519746212.43478212556-0.000987564733409-0.1772937950630.09588928765280.1934617279160.134066402964-0.283818182475-0.107713299430.269826580171-0.1002158620050.2672337015840.0036513682704-0.02043927481210.190030890993-0.001748326609790.23052640695767.6696539222167.446870474294.850220272
31.83743895505-0.0654908059114-0.2285238762042.917972963860.8422091666193.36677889335-0.0657050430689-0.00304087540246-0.1408920258970.110366254816-0.01887345147890.09462751491670.220866410535-0.01989985368660.07687853710710.213227334268-0.001818087694130.0141552492750.112929576330.01419760881350.18814855600561.0513432042160.061000119287.223806786
43.57714167246-1.252296639370.2313659449233.990817036860.5092925301532.50774934122-0.392150854054-0.368761503966-0.3899384920680.9451665974160.1675756506860.2721281933580.634961142228-0.2397663480510.1915961441820.628679491412-0.09812580594290.1494020562990.2287339674420.03803569215780.4131632291352.6630804776148.908389338296.886362556
54.144277158980.8691374667681.594100083023.609718720880.111628611613.00246035132-0.0772289754196-0.765580415982-0.4130836811771.207697527730.03707544875620.4756460093151.09491943316-0.0730408337250.1145065506850.80150125503-0.0267612479670.1859836945870.2305478561490.14943065320.40740217503757.2493695046147.491861787302.360739153
63.31728665109-1.3930291466-0.759895427293.1210978821-0.04731514097682.937962180160.140635095050.3550863732170.0998471580614-0.451722544378-0.1596617223790.04742209020840.1152408474120.03696856906920.002274730512830.198670492968-0.00179182152442-0.01198196857980.20826297663-0.01484566392350.18018921772959.38989451166.650412186253.560981861
72.82674147479-1.970385098460.04969630011792.97219372178-0.4401327111490.7336032763260.01672203333320.1089646593810.10138912393-0.183939033322-0.06320039745060.01526554178330.1001091363470.03570175053180.0430767115080.134923501453-0.0109071032409-0.000317733187390.216363367684-0.008583045892220.21556376670558.7679824167170.637506276260.915748761
81.68814919405-0.499632884327-0.2150191728855.62914899851-0.900215825522.57935890168-0.0681654372187-0.0806471382064-0.04226953018160.04019726177230.0282008206554-0.1084250761920.289865539550.08477602770360.04188911144290.1269327004040.02243782218810.02788633279520.164751947558-0.005930653847280.1775244012363.0734919711162.649047535270.885260315
92.11122448491-0.2728717191230.3450304341713.49879803878-0.3143516083832.95134380311-0.07699457995850.267134114333-0.39352242493-0.3107903061130.009132238851380.1526406725630.543292590524-0.0361921085860.1091648362250.312434685477-0.03549047133070.02180300789340.165637664188-0.04280680443060.29217137367858.7977485668152.540283318259.705194725
106.5230125015-0.176312634578-0.6529349422553.77378017620.209905597783.6787459905-0.1852775503270.492769306981-1.32085979523-0.5574000132580.136146991520.2409816153720.8853084170340.03617163516250.07001757861370.5478535072880.00924664837980.07608127972470.190565483094-0.08525422335960.53991054201360.6001499207142.677596074258.92049094
112.5661231321-0.8835852661910.3578177804193.12531917778-0.0006138662773762.385017992730.1428885112030.71626179972-0.570876044841-0.946207313181-0.242618901924-0.08107549694760.7520356204986.02344044845E-60.1490733323440.6129984243340.01251711386080.03901541221110.30439898129-0.1824722031060.41999786470459.8793001083147.615185053250.328273039
123.66657057465-0.394196342159-0.9511902188156.45476916911.176591446135.01173298595-0.1427244082730.2362333090750.0395258230069-0.5169999849510.177464799805-0.521222339792-0.1098318609140.280233282607-0.09593177495870.41236458059-0.05115510562740.07205696231420.2625844806540.004519647044580.29461658039753.4367335892196.80871075283.703748929
132.171038894660.414651779774-0.2750181307123.48069394599-0.2632888956322.328223133460.06278933005320.002080934616290.24039485732-0.0818730409668-0.0214680611165-0.31343008409-0.5532098158330.176458127053-0.02214526342060.306880206951-0.05267844802780.02415112251060.177438101598-0.02512368438360.26688361459255.6940650563200.102577504293.420074283
144.206045740720.2577794762510.4376324796855.680434364771.348486604213.59959465288-0.0313108393037-0.1657687575660.02092422261610.5857506274010.01146293395-0.300979093115-0.2579128677540.2404771576240.01443996238780.251026642634-0.0385408391037-0.03454627629410.213097481731-0.0247124356670.22147805297958.4414222851192.887586692304.050567724
152.143661851920.4327460607690.6518427200812.132901812060.3477689715052.490942986610.0477234809273-0.1143112064610.1015409600340.049263277787-0.05736531090130.0064663092808-0.223242616563-0.2387755752040.006175875910540.2114468375920.008648371720920.03262736259280.210873014568-0.02200748930940.21232010046344.8356703501191.764312092298.699263009
163.19571125639-0.745653310324-0.2882090046354.47796281228-0.7147560042553.64290379615-0.0505444667364-0.06558364763350.07526379574990.04641192472280.103407016110.291784216992-0.0618630443008-0.556311447186-0.07093525851250.155435467345-0.00378946732012-0.02446795979330.310384752222-0.05218363186020.23093428893937.3396710318189.320513441291.968494373
172.91093160858-0.9986743017760.4911112538649.077801882680.4330402513221.569430248490.1115932199860.366271495707-0.537962566082-0.51492942419-0.2884437902590.1590627722210.500938466185-0.6048161140050.06443800722820.320528247072-0.1033216892540.02358862985990.375357132932-0.08869196797180.3395330549336.1629126674177.358397688287.377472637
183.08878940729-0.196118364632-0.1098268545659.958994965870.5015356816675.542474909270.1656075614650.4773422306860.100620645731-0.882879628929-0.00023637191837-0.181258223378-0.23178270539-1.02796304845-0.1888677158550.4505887966650.163844448779-0.008558339941240.9739649698880.04149373506160.29733245323945.1875283529159.34502916316.104127629
193.47866366362-0.0759899938305-0.657274209983.12226786977-0.09461018161794.547444691260.1885379513590.631756210117-0.1326111895450.0384088925123-0.2102206194170.3329012302590.0374066412891-1.30490895397-0.09703980314540.3785149212890.0642656129875-0.01380130149820.8908646221350.03666508826910.2935946967542.0442125649156.002372795324.788807976
203.9447891040.964153549728-0.4263374564234.06131371290.2048726710365.178496846870.377559894940.0682055786463-0.003794972021870.480299394901-0.2928021324220.0767646912487-0.280432127083-0.593219583638-0.1136523218110.4785571337150.01260655934260.001586616437190.5938572900610.07132449440030.23926420712146.8649859945159.388912947336.91362084
212.048478118851.59719263519-0.5476627590553.349239394131.421191320173.166557887190.2402756289390.04575966288-0.3139314482880.437281458108-0.244955066178-0.4093556586320.3291824205990.106560588318-0.05751821493790.4239992283040.0622296947408-0.08110612790220.489466109470.09678333437710.32236508395957.0025373228152.646408338327.935078774
223.168648074291.07324594537-1.436179187385.317026535650.4008103005855.421501905860.2562128035930.233114287801-0.0748053508287-0.0116821042651-0.103332089601-0.433899523379-0.2776832946980.409612947591-0.1743951283460.3616326584330.0821350653852-0.04784000812770.6156657277250.1344276444780.28884291310765.1089476821162.381184638324.917917695
233.8222745291.65850454136-0.5285170239125.35087860921.232697659524.20765436350.1722941951040.415056211101-0.1374336211490.0875745768437-0.0764112263316-0.542356502003-0.002913253708230.421631935908-0.1109882200490.3764889421610.1052342262330.007633140276360.6049336795490.09831007268320.29781282076864.4943722189159.491620435318.231437798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 172 )
10X-RAY DIFFRACTION10chain 'B' and (resid 173 through 187 )
11X-RAY DIFFRACTION11chain 'B' and (resid 188 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 28 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 85 )
14X-RAY DIFFRACTION14chain 'C' and (resid 86 through 108 )
15X-RAY DIFFRACTION15chain 'C' and (resid 109 through 172 )
16X-RAY DIFFRACTION16chain 'C' and (resid 173 through 202 )
17X-RAY DIFFRACTION17chain 'C' and (resid 203 through 224 )
18X-RAY DIFFRACTION18chain 'D' and (resid 4 through 28 )
19X-RAY DIFFRACTION19chain 'D' and (resid 29 through 85 )
20X-RAY DIFFRACTION20chain 'D' and (resid 86 through 126 )
21X-RAY DIFFRACTION21chain 'D' and (resid 127 through 159 )
22X-RAY DIFFRACTION22chain 'D' and (resid 160 through 187 )
23X-RAY DIFFRACTION23chain 'D' and (resid 188 through 221 )

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