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

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Basic information

Entry
Database: PDB / ID: 5evk
TitleCrystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor L-CS319
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / inhibitor / carbapenemase / antibiotic resistance
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 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3C7 / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.627 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 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
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_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,3595
Polymers28,8951
Non-polymers4644
Water5,999333
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,71810
Polymers57,7892
Non-polymers9288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Unit cell
Length a, b, c (Å)104.980, 104.980, 98.465
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-598-

HOH

31A-720-

HOH

41A-790-

HOH

51A-831-

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-3C7 / (3R,5R,7aS)-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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
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: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.627→30.872 Å / Num. obs: 40522 / % possible obs: 99.69 % / Redundancy: 65.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 41.04
Reflection shellResolution: 1.627→1.66 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 6 / % possible all: 94.1

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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: 1.627→30.872 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 1979 4.88 %
Rwork0.1574 --
obs0.1586 40522 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.627→30.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 20 333 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162082
X-RAY DIFFRACTIONf_angle_d1.5732844
X-RAY DIFFRACTIONf_dihedral_angle_d13.693767
X-RAY DIFFRACTIONf_chiral_restr0.095316
X-RAY DIFFRACTIONf_plane_restr0.009374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6272-1.66790.24261460.21862604X-RAY DIFFRACTION96
1.6679-1.71290.25031470.20012684X-RAY DIFFRACTION100
1.7129-1.76330.24591300.19862713X-RAY DIFFRACTION100
1.7633-1.82030.22591370.18322731X-RAY DIFFRACTION100
1.8203-1.88530.18741180.18282720X-RAY DIFFRACTION100
1.8853-1.96080.21561280.17412739X-RAY DIFFRACTION100
1.9608-2.050.19491390.17072737X-RAY DIFFRACTION100
2.05-2.1580.2111360.15992734X-RAY DIFFRACTION100
2.158-2.29320.18081660.14852733X-RAY DIFFRACTION100
2.2932-2.47020.16161500.15072728X-RAY DIFFRACTION100
2.4702-2.71870.16031260.15372801X-RAY DIFFRACTION100
2.7187-3.11170.181340.15752800X-RAY DIFFRACTION100
3.1117-3.91920.15911500.13812833X-RAY DIFFRACTION100
3.9192-30.87710.17351720.15022986X-RAY DIFFRACTION100

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