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

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Basic information

Entry
Database: PDB / ID: 5evd
TitleCrystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor D-VC26
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-VC2 / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,4836
Polymers28,8951
Non-polymers5885
Water4,882271
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)117,93224
Polymers115,5784
Non-polymers2,35320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)105.130, 105.130, 98.170
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-507-

HOH

21A-740-

HOH

31A-768-

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-VC2 / (3S,5S,7aR)-2,2-dimethyl-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid


Mass: 265.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO2S3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 271 / 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: 54.61 %
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: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→30.35 Å / Num. obs: 30208 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 21.69
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 34.9 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 4.29 / % possible all: 100

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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: 1.8→30.348 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 1466 4.85 %
Rwork0.1655 --
obs0.167 30203 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 27 271 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082091
X-RAY DIFFRACTIONf_angle_d1.0482860
X-RAY DIFFRACTIONf_dihedral_angle_d12.596739
X-RAY DIFFRACTIONf_chiral_restr0.048317
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.2551580.25072795X-RAY DIFFRACTION100
1.8643-1.9390.24531620.21612792X-RAY DIFFRACTION100
1.939-2.02720.23261220.18812863X-RAY DIFFRACTION100
2.0272-2.13410.21051470.18332808X-RAY DIFFRACTION100
2.1341-2.26770.19221190.17212861X-RAY DIFFRACTION100
2.2677-2.44270.20711490.16922858X-RAY DIFFRACTION100
2.4427-2.68840.19821580.16582845X-RAY DIFFRACTION100
2.6884-3.07710.16841350.16442895X-RAY DIFFRACTION100
3.0771-3.87560.17751500.14432934X-RAY DIFFRACTION100
3.8756-30.35270.18991660.14993086X-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)
15.06543.8191-0.93353.1394-1.18511.6148-0.0838-0.5126-0.2937-0.0771-0.0088-0.1170.29480.76610.06750.34640.1289-0.04510.3678-0.05320.2186-6.476424.2492-14.9638
21.52330.3301-0.47850.8995-0.08512.09030.00830.020.0149-0.24160.17080.21240.5002-0.1189-0.17490.3296-0.072-0.13030.19090.05880.2354-36.07920.3044-6.7462
31.41721.0780.29081.44541.19771.59930.09360.18560.1281-0.24910.1410.43260.2451-0.2368-0.17260.2514-0.0744-0.1190.23060.11350.2619-35.6728.6593-9.1864
40.90390.0989-0.10781.3940.1692.01760.07150.06670.0577-0.07550.09910.09670.09190.0934-0.16240.1924-0.0229-0.03150.14030.02540.1865-27.466336.5355-9.0647
52.84020.96410.26571.9675-0.12421.44210.0898-0.12550.16040.15050.05070.3050.077-0.0901-0.12050.18-0.0124-0.00120.12710.01350.2194-31.376632.7034.7219
64.96821.0462-0.95222.3533-0.32572.36970.1573-0.36360.45710.2285-0.00150.3636-0.10010.1193-0.14260.1947-0.01020.00630.1369-0.01790.1817-28.112232.676911.9786
70.9368-0.8096-1.16640.9590.32393.41890.0409-0.0495-0.1654-0.05110.05760.11070.56720.0103-0.07870.3292-0.027-0.06780.20670.02570.1906-31.930415.85016.391
86.2813.63770.60883.3988-0.20050.96230.0066-0.3258-0.01470.1484-0.1151-0.10650.09850.32540.11450.27340.0084-0.0190.3150.00560.146-17.299928.290214.5574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 239 )
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 261 )
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 295 )
8X-RAY DIFFRACTION8chain 'A' and (resid 296 through 317 )

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