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- PDB-5evb: Crystal structure of the metallo-beta-lactamase L1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5evb
TitleCrystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor D-CS319
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / inhibitor / carbapenemase / antibiotic resistance
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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3R9 / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 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: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes.
Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Apr 14, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 10, 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)29,4556
Polymers28,8951
Non-polymers5605
Water5,855325
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)117,82024
Polymers115,5784
Non-polymers2,24120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)104.957, 104.957, 98.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-514-

HOH

31A-601-

HOH

41A-788-

HOH

51A-792-

HOH

61A-803-

HOH

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Components

#1: Protein 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)
Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / 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-3R9 / (3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid


Mass: 237.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO2S3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 277.15 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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.84→28.97 Å / Num. obs: 28142 / % possible obs: 99.4 % / Redundancy: 37.9 % / Rmerge(I) obs: 0.213 / Net I/σ(I): 16.9
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 6 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SML

1sml


Resolution: 1.841→28.968 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 1376 4.89 %
Rwork0.1479 --
obs0.1501 28141 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.841→28.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 25 325 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072080
X-RAY DIFFRACTIONf_angle_d1.0442843
X-RAY DIFFRACTIONf_dihedral_angle_d12.575737
X-RAY DIFFRACTIONf_chiral_restr0.046316
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8412-1.9070.26111370.20272459X-RAY DIFFRACTION94
1.907-1.98330.2161510.17382625X-RAY DIFFRACTION100
1.9833-2.07350.19841420.16242629X-RAY DIFFRACTION100
2.0735-2.18280.1991350.15342653X-RAY DIFFRACTION100
2.1828-2.31950.18821390.14432651X-RAY DIFFRACTION100
2.3195-2.49850.19691460.1492664X-RAY DIFFRACTION100
2.4985-2.74980.20111490.14742668X-RAY DIFFRACTION100
2.7498-3.14730.1921290.15262712X-RAY DIFFRACTION100
3.1473-3.96360.19331140.13432772X-RAY DIFFRACTION100
3.9636-28.97130.17331340.1382932X-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)
13.54531.3291-3.19510.8188-1.13222.99990.0305-0.26390.2093-0.14580.08290.05820.35520.2234-0.0760.2370.0127-0.06940.1659-0.02020.1421-24.192919.8726-8.0767
23.70630.3498-0.82690.84020.25352.36850.01690.13360.0349-0.35890.140.28630.3427-0.1551-0.13150.2469-0.0609-0.11020.12290.06030.1897-36.606822.147-8.7183
31.84341.4580.48381.77751.59522.93050.00880.15920.2084-0.23690.11310.44550.2076-0.2232-0.09150.1772-0.0543-0.08020.1360.09310.1925-35.040629.3635-9.2794
40.91140.0617-0.01721.21190.17751.80320.05650.07460.0615-0.0810.07830.07830.08730.0794-0.1280.1395-0.0237-0.02610.10520.02730.1492-27.422336.4308-9.1504
56.02812.99962.58051.49921.38662.9805-0.3161-0.12990.53920.0548-0.08950.8624-0.0152-0.32660.23140.1221-0.00960.05150.15410.03330.4346-41.857635.88821.5104
67.37762.5492-1.56161.4983-0.64352.11380.0851-0.18260.06440.06060.09580.32280.1567-0.2405-0.11830.1399-0.0313-0.01510.12020.05550.2202-37.699428.78955.6045
76.98132.1812-0.47497.1446-0.87982.16640.0296-0.05270.03680.1865-0.0271-0.4320.04450.19490.01520.13-0.0093-0.01510.1371-0.01640.0701-15.011336.14175.4107
87.42672.7741-0.63053.9863-0.25342.55370.1631-0.48560.49630.2317-0.07690.4635-0.09710.0576-0.06540.1416-0.00030.00430.0954-0.00660.1273-28.178932.67911.9893
92.27030.2962-1.17672.39950.44622.74790.0860.0149-0.1854-0.0830.11340.16880.6424-0.0763-0.15120.2521-0.0263-0.05570.1230.02760.1196-31.657515.75756.5508
103.46664.45340.12935.7724-0.06090.83170.2017-0.34290.02330.164-0.2188-0.12480.11970.30330.02360.19510.0046-0.02010.25560.0280.0779-17.338728.267114.6435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 191 )
6X-RAY DIFFRACTION6chain 'A' and (resid 193 through 219 )
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 239 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 261 )
9X-RAY DIFFRACTION9chain 'A' and (resid 262 through 295 )
10X-RAY DIFFRACTION10chain 'A' and (resid 296 through 317 )

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