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- PDB-7zo7: L1 metallo-beta-lactamase in complex with hydrolysed cefmetazole -

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Basic information

Entry
Database: PDB / ID: 7zo7
TitleL1 metallo-beta-lactamase in complex with hydrolysed cefmetazole
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-JOU / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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)29,6115
Polymers28,8951
Non-polymers7164
Water4,107228
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)118,44420
Polymers115,5784
Non-polymers2,86616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3
MethodPISA
Unit cell
Length a, b, c (Å)105.469, 105.469, 98.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-622-

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-JOU / (2R,5R)-2-[(1S)-1-[2-(cyanomethylsulfanyl)ethanoylamino]-1-methoxy-2-oxidanyl-2-oxidanylidene-ethyl]-5-[(1-methyl-1,2,3,4-tetrazol-5-yl)sulfanylmethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / hydrolysed cefmetazole


Mass: 489.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N7O6S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
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: 0.97633 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.629→91.4 Å / Num. obs: 40756 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 17.6
Reflection shellResolution: 1.629→1.67 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2980 / CC1/2: 0.667 / Rpim(I) all: 0.705

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0O

7o0o


Resolution: 1.63→66.86 Å / SU ML: 0.1601 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 2050 5.04 %
Rwork0.159 38623 -
obs0.1598 40673 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.63→66.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 38 228 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792133
X-RAY DIFFRACTIONf_angle_d1.00852921
X-RAY DIFFRACTIONf_chiral_restr0.0579322
X-RAY DIFFRACTIONf_plane_restr0.0076386
X-RAY DIFFRACTIONf_dihedral_angle_d13.3593760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.26661250.24952502X-RAY DIFFRACTION98.02
1.67-1.710.27691540.22522502X-RAY DIFFRACTION99.81
1.71-1.750.26921320.2182539X-RAY DIFFRACTION99.78
1.75-1.810.32131170.25462525X-RAY DIFFRACTION99.7
1.81-1.860.23361290.21272551X-RAY DIFFRACTION99.85
1.86-1.930.20971120.17092558X-RAY DIFFRACTION99.93
1.93-2.010.171360.15282557X-RAY DIFFRACTION99.89
2.01-2.10.15891450.15352546X-RAY DIFFRACTION100
2.1-2.210.17631270.162552X-RAY DIFFRACTION99.85
2.21-2.350.19171380.15392577X-RAY DIFFRACTION100
2.35-2.530.17981540.14572570X-RAY DIFFRACTION99.96
2.53-2.790.1531390.14542580X-RAY DIFFRACTION100
2.79-3.190.17661380.15612615X-RAY DIFFRACTION99.96
3.19-4.020.14861440.13792642X-RAY DIFFRACTION100
4.02-66.860.16191600.15792807X-RAY DIFFRACTION99.9
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)
11.533150193940.50518168879-1.411482396780.781047160273-0.5190860653241.90359710767-0.0441226029001-0.05433667054190.00454232508669-0.149870270850.1154399764330.09268874280460.3512276142090.0167180729057-0.06143861910990.320841949969-0.043417468086-0.08029771253370.2189790960460.01692571255050.23148991391-30.38663620421.1309093065-8.29753491791
24.388173999062.636290825140.473677791893.214748676181.327804838762.83775591138-0.08229825822160.1605697405470.344373534284-0.2470347478340.1500447481260.4335803964090.137000496881-0.323505808899-0.07444023696610.218120531869-0.0535455686113-0.06577345268770.1773120756330.08621862370630.198472429999-35.606369282528.6998370735-9.28240742564
31.01933436917-0.0625078095622-0.3637188725051.261061557860.289666034191.95373322790.06863022950540.06416026781290.0745407495256-0.10814693610.06083141112890.04918556558230.06069479383390.0872400130235-0.1311494236110.219120507275-0.0289700934703-0.02278546336670.1931068400470.0246734258690.213466709065-27.24323720936.6066336926-9.02529533403
46.618070320431.82789097350.7545254227432.302347988570.1953916055671.195132957710.106171083095-0.1565689930810.03741462369240.1122784425740.002492451257870.2202832691260.044989985733-0.0491044211904-0.08567449689120.170425128898-0.0106364901163-0.001364216431930.1298650507390.02069491392310.153106586119-31.285544677832.77027894684.69730482291
56.327994784872.371399102-2.439239201022.68864599507-1.000031922543.653344229820.256849887356-0.4462768055880.3542482030760.188840170888-0.1320866956630.259884901915-0.1090695702450.116219270205-0.1337119668850.2156889299960.00451934175504-0.008970305101320.1529449480160.002150668659960.185786354865-28.338112179732.684183216912.2872833428
63.66299812137-0.143643382482-0.3170074500781.473670067962.927761598096.909384478630.114278513709-0.0879456772556-0.1992323289810.161525127957-0.0130859664949-0.02118031677010.8214119108770.0350119905465-0.09414647875760.317533845363-0.00187702255069-0.04575575041530.1790333968240.03821805437810.184351749631-31.68968155315.80892618816.34641726106
75.188909343426.19079349970.3851882160157.416786894470.1572658701020.9492210185460.199101904046-0.61242219273-0.1931564394820.37086491247-0.218072408626-0.3031441935260.1158111887220.2690079817270.0522475190360.2489855690670.00469446402991-0.03667848702230.3285744850250.03104298803910.139401335829-17.347303998428.359941693114.5611161819
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 69 )2 - 691 - 68
22chain 'A' and (resid 70 through 92 )70 - 9269 - 91
33chain 'A' and (resid 93 through 143 )93 - 14392 - 142
44chain 'A' and (resid 144 through 201 )144 - 201143 - 200
55chain 'A' and (resid 202 through 223 )202 - 223201 - 222
66chain 'A' and (resid 224 through 245 )224 - 245223 - 244
77chain 'A' and (resid 246 through 267 )246 - 267245 - 266

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