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- PDB-7zo6: L1 metallo-beta-lactamase in complex with hydrolysed cefoxitin -

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Basic information

Entry
Database: PDB / ID: 7zo6
TitleL1 metallo-beta-lactamase in complex with hydrolysed cefoxitin
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-JNX / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 1.3Nov 13, 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)29,5675
Polymers28,8951
Non-polymers6724
Water3,207178
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)118,26820
Polymers115,5784
Non-polymers2,68916
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 area10110 Å2
ΔGint-87 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.345, 105.345, 97.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-578-

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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-JNX / (2~{R},5~{S})-5-(aminocarbonyloxymethyl)-2-[(1~{S})-1-methoxy-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid / hydrolysed cefoxitin


Mass: 445.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O8S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
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: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.61→66.74 Å / Num. obs: 42005 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 33.65 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 21.3
Reflection shellResolution: 1.61→1.64 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2063 / CC1/2: 0.566 / Rpim(I) all: 1.058 / % possible all: 99.9

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Processing

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

7o0o


Resolution: 1.61→45.62 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2120 5.05 %
Rwork0.164 39820 -
obs0.1653 41940 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.28 Å2 / Biso mean: 45.8766 Å2 / Biso min: 25.88 Å2
Refinement stepCycle: final / Resolution: 1.61→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 99 178 2271
Biso mean--54.75 45.89 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.61-1.650.35631350.379526072742
1.65-1.690.36961600.339925742734
1.69-1.730.29731430.299726012744
1.73-1.790.28921200.25826362756
1.79-1.840.30011250.232526292754
1.84-1.910.27181290.219526112740
1.91-1.990.24221320.186426452777
1.99-2.080.19821510.166326152766
2.08-2.190.18391350.153526392774
2.19-2.320.19061330.153326542787
2.32-2.50.2091590.150526432802
2.5-2.750.1851450.148826522797
2.75-3.150.16791450.156926952840
3.15-3.970.16931430.143927342877
3.97-45.620.17031650.158828853050
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)
10.5615-0.32420.19992.59341.71291.85180.0316-0.02180.172-0.0081-0.06810.0664-0.1445-0.33020.04940.36440.06970.03820.32910.03270.317633.428515.31339.5995
27.44974.70172.03247.4074.8515.03670.14020.23920.4802-0.2407-0.13150.2636-0.6006-0.2981-0.04640.41810.11740.05060.33530.06720.344535.191221.22922.9704
32.98090.09390.62288.7044-3.28566.53960.0337-0.02310.1177-0.1927-0.1009-0.5818-0.32150.160.05550.28110.06060.0680.2273-0.04870.266143.038315.5617.0729
41.983-0.33840.04831.18020.09451.53770.04820.02650.1248-0.0454-0.0349-0.00870.0506-0.0382-0.00350.31580.02030.01970.2534-0.01020.291546.82947.96189.4467
51.9051.3009-0.16128.72460.16341.42780.0469-0.21430.12090.3246-0.0018-0.0892-0.137-0.1273-0.02490.29080.04870.02180.278-0.01280.228241.9168.727321.8383
69.42657.58126.61786.17655.96576.38510.1067-0.5722-0.0260.4803-0.23590.29390.0764-0.26750.06650.3810.06030.03810.3830.01190.253243.25182.508629.2748
72.63711.44434.25892.9770.69338.7634-0.0385-0.20350.15390.25740.1907-0.0189-0.2792-0.5873-0.19560.36010.09390.06440.3629-0.01840.324732.619519.237623.5927
86.88754.6643-3.38913.7615-3.43823.2989-0.0078-0.2727-0.13130.3877-0.02020.0795-0.0228-0.230.0320.35910.04110.03240.39890.00610.284533.27180.83930.8175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )A2 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 70 )A57 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 92 )A71 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 156 )A93 - 156
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 201 )A157 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 215 )A202 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 245 )A216 - 245
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 267 )A246 - 267

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