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- PDB-7afz: L1 metallo-b-lactamase with compound EBL-1306 -

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Basic information

Entry
Database: PDB / ID: 7afz
TitleL1 metallo-b-lactamase with compound EBL-1306
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / inhibitor / lactamase / antibiotic resistance / indole
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-RBW / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHinchliffe, P. / Spencer, J. / Brem, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines InitiativeENABLE United Kingdom
CitationJournal: Nat.Chem. / Year: 2022
Title: Imitation of beta-lactam binding enables broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Brem, J. / Panduwawala, T. / Hansen, J.U. / Hewitt, J. / Liepins, E. / Donets, P. / Espina, L. / Farley, A.J.M. / Shubin, K. / Campillos, G.G. / Kiuru, P. / Shishodia, S. / Krahn, D. / ...Authors: Brem, J. / Panduwawala, T. / Hansen, J.U. / Hewitt, J. / Liepins, E. / Donets, P. / Espina, L. / Farley, A.J.M. / Shubin, K. / Campillos, G.G. / Kiuru, P. / Shishodia, S. / Krahn, D. / Lesniak, R.K. / Schmidt Adrian, J. / Calvopina, K. / Turrientes, M.C. / Kavanagh, M.E. / Lubriks, D. / Hinchliffe, P. / Langley, G.W. / Aboklaish, A.F. / Eneroth, A. / Backlund, M. / Baran, A.G. / Nielsen, E.I. / Speake, M. / Kuka, J. / Robinson, J. / Grinberga, S. / Robinson, L. / McDonough, M.A. / Rydzik, A.M. / Leissing, T.M. / Jimenez-Castellanos, J.C. / Avison, M.B. / Da Silva Pinto, S. / Pannifer, A.D. / Martjuga, M. / Widlake, E. / Priede, M. / Hopkins Navratilova, I. / Gniadkowski, M. / Belfrage, A.K. / Brandt, P. / Yli-Kauhaluoma, J. / Bacque, E. / Page, M.G.P. / Bjorkling, F. / Tyrrell, J.M. / Spencer, J. / Lang, P.A. / Baranczewski, P. / Canton, R. / McElroy, S.P. / Jones, P.S. / Baquero, F. / Suna, E. / Morrison, A. / Walsh, T.R. / Schofield, C.J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6236
Polymers28,8951
Non-polymers7295
Water4,378243
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


  • defined by author&software
  • Evidence: gel filtration, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 15030 ...Evidence: gel filtration, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 15030 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 39430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -481 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 104.78000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 104.78000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000
  • 118 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)118,49424
Polymers115,5784
Non-polymers2,91520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area10870 Å2
ΔGint-138 kcal/mol
Surface area39690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.780, 104.780, 98.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-421-

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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RBW / 3-[3-chloranyl-4-(methylsulfonylmethyl)phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid


Mass: 405.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20ClNO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 1 ul protein (15 mg/ml) mixed with 1 ul reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91584 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91584 Å / Relative weight: 1
ReflectionResolution: 1.5→66.62 Å / Num. obs: 51300 / % possible obs: 100 % / Redundancy: 68.8 % / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/σ(I): 23.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 56.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2506 / CC1/2: 0.564 / Rpim(I) all: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EVD

5evd


Resolution: 1.5→66.617 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 2543 4.96 %
Rwork0.1523 48705 -
obs0.1531 51248 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.53 Å2 / Biso mean: 28.3289 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.5→66.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 58 243 2302
Biso mean--51.59 34.27 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082099
X-RAY DIFFRACTIONf_angle_d0.9332874
X-RAY DIFFRACTIONf_chiral_restr0.053313
X-RAY DIFFRACTIONf_plane_restr0.008376
X-RAY DIFFRACTIONf_dihedral_angle_d10.7281231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.52890.31611320.28272668
1.5289-1.56010.27661450.25922655
1.5601-1.5940.23351380.23632661
1.594-1.63110.24561330.2112660
1.6311-1.67190.24811380.19772675
1.6719-1.71710.20171400.18062657
1.7171-1.76760.21921360.17392656
1.7676-1.82470.1651550.16172670
1.8247-1.88990.19381540.15542675
1.8899-1.96560.19271250.13652690
1.9656-2.0550.15311230.13172711
2.055-2.16340.15571490.13762678
2.1634-2.29890.14471330.1312709
2.2989-2.47640.17211360.12622721
2.4764-2.72570.15481600.13352711
2.7257-3.12010.13581510.14342751
3.1201-3.93090.15141420.13522785
3.9309-66.6170.15071530.15762972
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)
11.1568-1.4871-1.48893.91113.95024.37640.3154-0.1058-0.02771.1047-0.25650.04020.6671-0.5020.08140.3001-0.067-0.02320.39280.07530.190324.0298-6.01462.0019
21.6591-0.20130.32572.19070.632.14910.16810.08510.2793-0.24230.0221-0.1803-0.3537-0.215-0.14680.2670.06690.09840.15130.06070.207437.324521.46878.6274
31.504-0.37170.23250.77190.00281.42750.04190.02150.16-0.05680.0585-0.13140.0021-0.0201-0.08590.15860.01560.03150.10290.00430.153445.37638.04599.6065
41.36510.4364-0.28383.89440.40221.3430.0535-0.13680.14560.0920.0565-0.1357-0.0833-0.0743-0.070.14190.03640.010.14070.00160.149341.64958.778821.8246
52.11480.43970.30815.81230.63652.36060.0654-0.23170.17550.33320.0756-0.49530.0570.0017-0.0980.13730.0314-0.00230.1558-0.01720.137642.26788.035228.2637
62.04040.06230.97651.80620.00543.19480.0273-0.06570.21060.0940.0734-0.0218-0.2748-0.4613-0.10470.20360.06990.04750.20430.02490.150329.560119.639122.7695
74.22983.7184-0.79253.2864-0.63221.0137-0.0114-0.0895-0.11140.39220.0323-0.13870.1289-0.2153-0.00010.26030.00510.02090.20750.00540.149833.02770.917430.8888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )A2 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 81 )A15 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 156 )A82 - 156
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 201 )A157 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 223 )A202 - 223
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 245 )A224 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 267 )A246 - 267

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