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- PDB-7a63: Crystal structure of L1 with hydrolyzed faropenem (imine, ring-cl... -

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Basic information

Entry
Database: PDB / ID: 7a63
TitleCrystal structure of L1 with hydrolyzed faropenem (imine, ring-closed form)
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / metallo-beta-lactamase / antibiotic / faropenem / catalysis
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
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-R3N / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57000109226 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6828
Polymers28,8951
Non-polymers7887
Water3,855214
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,72932
Polymers115,5784
Non-polymers3,15128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)105.300, 105.300, 98.099
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-303-

ZN

21A-409-

HOH

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Components

#1: Protein Metallo-beta-lactamase L1 / Class B3 metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28894.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: P52700, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-R3N / (2R,5S)-2-[(1S,2R)-1-carboxy-2-hydroxy-propyl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydrothiazole-4-carboxylic acid / (2~{R},5~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-[(2~{R})-oxolan-2-yl]-1,3-thiazolidine-4-carboxylic acid


Mass: 303.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 2 ul protein (15 mg/ml) mixed with 2 ul reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.57→52.65 Å / Num. obs: 45278 / % possible obs: 100 % / Redundancy: 72.9 % / Biso Wilson estimate: 24.4760197843 Å2 / CC1/2: 0.911 / Rpim(I) all: 0.012 / Net I/σ(I): 32.3
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 2194 / CC1/2: 0.846 / Rpim(I) all: 0.552 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SML

1sml


Resolution: 1.57000109226→52.65 Å / SU ML: 0.15001859961 / Cross valid method: FREE R-VALUE / σ(F): 1.34352566284 / Phase error: 23.2433365783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192818172569 2337 5.17104040359 %
Rwork0.169183211044 42857 -
obs0.170409688506 45194 99.9027366373 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.8090325092 Å2
Refinement stepCycle: LAST / Resolution: 1.57000109226→52.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 38 214 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876502500642145
X-RAY DIFFRACTIONf_angle_d1.071456145982942
X-RAY DIFFRACTIONf_chiral_restr0.0557431350773325
X-RAY DIFFRACTIONf_plane_restr0.00741334868501388
X-RAY DIFFRACTIONf_dihedral_angle_d15.2513303847766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57000109226-1.6020.325916638741280.2935990893072482X-RAY DIFFRACTION99.9234303216
1.602-1.63690.3246689608281360.2698735794052456X-RAY DIFFRACTION99.57741068
1.6369-1.6750.2936195525181360.2499161252152477X-RAY DIFFRACTION99.7709049255
1.675-1.71690.2943461985471330.2470274403742473X-RAY DIFFRACTION99.9233128834
1.7169-1.76330.2527229060631320.2311946045062465X-RAY DIFFRACTION99.807840123
1.7633-1.81520.2703309832011240.2314083557892515X-RAY DIFFRACTION99.810892587
1.8152-1.87380.2783777934691300.2120487176422486X-RAY DIFFRACTION99.8092331171
1.8738-1.94070.2357299923741430.1978066964782486X-RAY DIFFRACTION99.9239832763
1.9407-2.01840.2082416929041450.1909984838262477X-RAY DIFFRACTION100
2.0184-2.11030.213042717361350.1795648143952520X-RAY DIFFRACTION99.9247271359
2.1103-2.22160.1817084646821410.1700352355332492X-RAY DIFFRACTION99.9240986717
2.2216-2.36080.1824502608371390.161108924282523X-RAY DIFFRACTION100
2.3608-2.5430.1663391326771470.1498994984412518X-RAY DIFFRACTION100
2.543-2.79890.1764988025651310.1500198240692556X-RAY DIFFRACTION100
2.7989-3.20390.1908211502531470.1644425647672563X-RAY DIFFRACTION100
3.2039-4.03630.1754290108461410.1473805763592599X-RAY DIFFRACTION99.9635169646
4.0363-52.650.1710657067711490.1604687007722769X-RAY DIFFRACTION100
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)
10.9045329981320.495976421375-1.592727633781.83726925104-0.8776431920122.327940165740.11215764392-0.2181150490590.08306077900740.1470838235520.09412220835440.2857385667680.005087413062080.0464438099409-0.1806713430690.240444702879-0.0343122073316-0.01181707134680.258550314790.04401104033940.220056971708-25.039448420220.0341914664-7.76085504238
22.2783313631-0.477797663464-0.6458204038282.884745854510.01224027495762.40177348745-0.1219903385510.0192137776373-0.187691553531-0.1483177832180.3569296420770.7929908609750.15139392451-0.350845231776-0.2256210210580.226314593342-0.0708407829908-0.02753159476220.3171025506740.1540622385380.363956152326-36.285458320821.8888692569-8.49970013053
33.817440868750.9939405704860.1719675144833.786029721821.044115115392.05148098036-0.1477211117130.2166107498920.106909443748-0.1360968069840.3178700099820.765218483380.0668169941181-0.430703023673-0.1449476737210.182311533093-0.0678168439633-0.02599418110340.3226529512250.1425473974410.284806020804-34.917620631129.2957473971-9.3194100075
41.14426429086-0.8776817320480.2028996321092.8723756751-0.09398395970891.60466434667-0.174010357473-0.143020822523-0.1072206624810.08206456976540.2929083798270.3319260435810.00931162654524-0.0732589221209-0.1037807937550.175346221506-0.02447380629510.01454417284890.2564392067320.06726169518940.169459464836-30.111884111736.4306593722-6.94868347614
53.224514179810.0758179317215-0.570941901482.87034523751-0.3501098873451.56041422296-0.273005259684-0.331946097344-0.1865972227390.5176703958080.3957083451350.322581725390.112901954559-0.102400521382-0.1086603589080.3090705053120.1042685888010.06752096096570.3258972469570.09953160010110.197868030898-28.542936305231.83899934495.45410116611
62.08883455993.06398005012-7.507432428573.5221103058-3.634977716416.94687007267-0.256147457799-0.5803746613930.4275099030180.9805210786540.4942497976070.318791242773-0.4066049365440.0465023549202-0.1915896669890.5178618274730.2138980101350.02777692972360.4780660457160.03006019348530.21472279026-24.545762342235.818739088813.4664108979
71.58723563527-0.331968392648-1.001001528271.39672196831.275830147393.49549082158-0.105533208182-0.183296105274-0.1552437776230.5898508755770.3314496549670.5178880682980.343977409386-0.0673513210201-0.1811375754330.3878129609610.1032861059070.1171548520360.4429487151360.1999002208180.33572231719-32.973773052618.54107778737.42036358568
87.653640632013.670620868130.3326474989463.58462822362-0.06908722786630.617356105847-0.0228162627744-0.588434555713-0.3048943178450.652177428660.131000267295-0.163868519070.167918533830.0274247477306-0.1187691364510.4722309328270.1740793222350.005111109603390.5021179817550.0939904343420.246224800972-17.352749457128.244809509814.5153378877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 201 )
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 215 )
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 245 )
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 267 )

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