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- PDB-7zo5: L1 metallo-beta-lactamase in complex with a mecillinam degradatio... -

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Basic information

Entry
Database: PDB / ID: 7zo5
TitleL1 metallo-beta-lactamase in complex with a mecillinam degradation product
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / antibiotic / ligand / zinc
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-JO9 / 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 2.0Sep 20, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _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 2.1Feb 7, 2024Group: Refinement description / Category: 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)29,5616
Polymers28,8951
Non-polymers6665
Water5,441302
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)118,24424
Polymers115,5784
Non-polymers2,66620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area10710 Å2
ΔGint-138 kcal/mol
Surface area39730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.610, 105.610, 98.450
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-407-

HOH

21A-611-

HOH

31A-626-

HOH

41A-655-

HOH

51A-658-

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-JO9 / (2~{R},4~{S})-2-[(1~{R})-2-(azepan-1-yl)-1-formamido-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / mecillinam degradation product


Mass: 343.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O4S / 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.: 302 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
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: I24 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.43→49.22 Å / Num. obs: 60073 / % possible obs: 100 % / Redundancy: 38 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 14.2
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 36.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2910 / CC1/2: 0.355 / Rpim(I) all: 1.832 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0O

7o0o


Resolution: 1.43→46.53 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 2915 4.86 %
Rwork0.1585 57059 -
obs0.1595 59974 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 36.4572 Å2 / Biso min: 18.99 Å2
Refinement stepCycle: final / Resolution: 1.43→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 108 304 2413
Biso mean--56.32 43.77 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.450.35641230.37082617274099
1.45-1.480.37781360.35152656279299
1.48-1.510.34211400.3342678281899
1.51-1.530.30011450.289226702815100
1.53-1.570.2911450.286126482793100
1.57-1.60.28361280.258427032831100
1.6-1.640.26381500.241826602810100
1.64-1.680.26911450.221626922837100
1.68-1.720.24561440.211626842828100
1.72-1.770.22271260.194426962822100
1.77-1.830.24991460.188526942840100
1.83-1.90.22011360.17527022838100
1.9-1.970.21131490.160526912840100
1.97-2.060.19971400.148927212861100
2.06-2.170.19261400.143227042844100
2.17-2.310.14011230.138527532876100
2.31-2.490.17361180.139227552873100
2.49-2.740.14571610.138427422903100
2.74-3.130.17971330.148427832916100
3.13-3.940.14491550.132828002955100
3.94-46.530.15821320.151730103142100
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)
12.8572-1.6221-2.79191.9982.73543.8943-0.2397-0.3297-0.09850.19110.18290.18890.3353-0.0180.03780.2418-0.0196-0.02270.32730.0280.23685.248531.008824.7571
25.3945-1.4252-0.33134.65460.76293.00880.08550.07180.3218-0.177-0.06140.3798-0.1232-0.3635-0.02110.11850.00430.01080.24940.00750.1883.48143.43624.0327
30.54490.40240.13721.13050.00721.34330.0377-0.07870.0497-0.0599-0.032-0.02370.08650.0273-0.01080.12550.0120.00980.235-0.00350.162418.139842.38923.9093
43.3443-1.93390.74813.7232-0.50221.42340.0178-0.37680.06550.18140.00020.2328-0.0541-0.14-0.00190.1401-0.03370.03480.2721-0.01430.17112.730443.584337.5747
56.5449-5.5307-1.31926.75351.73774.0865-0.1605-0.66210.15380.44590.1703-0.00860.00830.02820.00270.1918-0.07680.04250.31090.01990.149914.21240.811245.1465
63.092-2.06671.57643.96472.83686.69550.0332-0.3874-0.29190.15250.01240.4650.3653-0.8244-0.06050.1848-0.06490.03850.4050.03140.2444-2.104235.366439.1803
77.6-3.74240.73397.6908-2.84491.14750.1595-0.4159-0.17240.1017-0.1793-0.1140.1607-0.08510.02410.2888-0.03750.01470.40110.04840.221615.955529.227547.3919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )A2 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 92 )A33 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 143 )A93 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 201 )A144 - 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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