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- PDB-7zo3: L1 metallo-beta-lactamase in complex with hydrolysed tebipenem -

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Basic information

Entry
Database: PDB / ID: 7zo3
TitleL1 metallo-beta-lactamase in complex with hydrolysed tebipenem
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / antibiotic / ligand / zinc
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-JNQ / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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: J.Biol.Chem. / Year: 2023
Title: Interactions of hydrolyzed beta-lactams with the L1 metallo-beta-lactamase: Crystallography supports stereoselective binding of cephem/carbapenem products.
Authors: Hinchliffe, P. / Calvopina, K. / Rabe, P. / Mojica, M.F. / Schofield, C.J. / Dmitrienko, G.I. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionApr 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,7157
Polymers28,8951
Non-polymers8216
Water4,342241
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)118,86128
Polymers115,5784
Non-polymers3,28224
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 area11500 Å2
ΔGint-169 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.274, 105.274, 98.241
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-408-

HOH

21A-423-

HOH

31A-638-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-JNQ / (2S,3R,4S)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[1-(4,5-dihydro-1,3-thiazol-2-yl)azetidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / hydrolysed tebipenem


Mass: 401.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 54.77 %
Crystal growTemperature: 277 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: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.43→66.83 Å / Num. obs: 59030 / % possible obs: 99.2 % / Redundancy: 20.5 % / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 18
Reflection shellResolution: 1.43→1.46 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2865 / CC1/2: 0.305 / Rpim(I) all: 1.138 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0O

7o0o


Resolution: 1.43→66.83 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 2756 4.86 %
Rwork0.1732 53977 -
obs0.1744 56733 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.75 Å2 / Biso mean: 39.896 Å2 / Biso min: 21.92 Å2
Refinement stepCycle: final / Resolution: 1.43→66.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 64 241 2306
Biso mean--57.8 43.21 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.460.4258480.45721035108337
1.46-1.480.42041170.41152296241383
1.48-1.510.42391380.39432703284197
1.51-1.540.34461550.37112726288199
1.54-1.570.34481270.33382763289098
1.57-1.610.30881430.29872733287698
1.61-1.650.27871580.28292757291599
1.65-1.70.26731530.24812775292899
1.7-1.750.26141400.22962747288799
1.75-1.80.23771440.22382785292999
1.8-1.870.22651400.21712787292799
1.87-1.940.23191380.19722800293899
1.94-2.030.24891630.17762792295599
2.03-2.140.21061390.17482803294299
2.14-2.270.191290.172528442973100
2.27-2.450.18251260.165428732999100
2.45-2.690.1761630.158428312994100
2.69-3.080.20381410.158728863027100
3.08-3.880.16841570.139329243081100
3.88-66.830.16071370.150831173254100
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)
10.3342-0.3765-0.011.5831.00791.48570.16820.05310.1724-0.114-0.0266-0.1002-0.2323-0.383-0.13180.34880.09380.07980.35560.10530.275233.537916.09178.0497
21.4508-0.91191.19795.9658-1.43354.05350.07620.15660.2432-0.30520.0912-0.5753-0.3768-0.0521-0.15150.27670.06590.13990.19610.03710.237242.997815.63247.1169
31.4888-0.35160.181.09440.29911.52210.09570.03870.2105-0.05620.0492-0.1606-0.0226-0.0399-0.13410.2620.02710.04410.22760.01390.284646.82717.98579.448
40.930.5428-0.33332.29360.29941.47930.0618-0.10240.0920.11230.111-0.2062-0.1328-0.1045-0.15820.26980.04770.01750.25290.01970.272741.90058.787721.8905
59.41517.01236.31286.07636.76019.00360.1942-0.3597-0.06820.0698-0.1881-0.1940.3016-0.2191-0.02430.26290.0488-0.02330.2650.0320.187543.3532.692929.4571
61.39190.10541.52433.18281.20894.96610.08880.00240.12030.02420.0546-0.1377-0.3048-0.4943-0.12660.3070.08920.06630.31120.05410.251932.389619.813823.7714
77.02515.0711-1.58313.8374-0.66821.59720.0188-0.0857-0.1030.61230.0481-0.09180.2641-0.3184-0.02950.38690.00340.00050.3630.03490.204933.28880.937230.9133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 70 )A2 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 92 )A71 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 156 )A93 - 156
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 201 )A157 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 215 )A202 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 245 )A216 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 267 )A246 - 267

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