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- PDB-7zo2: L1 metallo-beta-lactamase complex with hydrolysed doripenem -

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Basic information

Entry
Database: PDB / ID: 7zo2
TitleL1 metallo-beta-lactamase complex with hydrolysed doripenem
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / antibiotic / ligand / zinc
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-DQM / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6927
Polymers28,8951
Non-polymers7976
Water4,071226
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)118,76628
Polymers115,5784
Non-polymers3,18824
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 area11330 Å2
ΔGint-177 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.435, 105.435, 98.181
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-401-

HOH

21A-412-

HOH

31A-589-

HOH

41A-625-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 232 molecules

#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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DQM / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Doripenem


Mass: 438.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 54.88 %
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: 1.49→66.86 Å / Num. obs: 52983 / % possible obs: 100 % / Redundancy: 38.4 % / CC1/2: 1 / Rpim(I) all: 0.015 / Net I/σ(I): 22.3
Reflection shellResolution: 1.49→1.52 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2586 / CC1/2: 0.563 / Rpim(I) all: 1.425

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Processing

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

7o0o


Resolution: 1.49→66.86 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 2599 4.92 %
Rwork0.1764 50178 -
obs0.1777 52777 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.85 Å2 / Biso mean: 42.9497 Å2 / Biso min: 17.06 Å2
Refinement stepCycle: final / Resolution: 1.49→66.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 65 226 2283
Biso mean--86.68 43.08 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.520.4521530.44642570272399
1.52-1.550.39271130.40262604271799
1.55-1.580.39161180.37052597271599
1.58-1.610.28251340.31325802714100
1.61-1.650.29411550.28062582273799
1.65-1.690.30951300.258526122742100
1.69-1.740.27431380.236125872725100
1.74-1.790.26361270.221226452772100
1.79-1.850.24281450.211325852730100
1.85-1.910.24211470.211925902737100
1.91-1.990.22211390.185526372776100
1.99-2.080.20371340.183326252759100
2.08-2.190.20371340.178426412775100
2.19-2.330.20071560.17826292785100
2.33-2.50.19471420.174926582800100
2.5-2.760.20991320.167626712803100
2.76-3.160.21111340.171427082842100
3.16-3.980.18751410.147627382879100
3.98-66.860.16121270.153729193046100
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)
10.19-0.3711-0.18011.15680.87160.5607-0.0577-0.0870.10510.35520.14660.00650.1018-0.0968-0.08420.41890.0633-0.01980.36670.02110.285429.690112.16188.7993
23.80320.79430.3574.51281.76413.2916-0.0577-0.00960.4517-0.10380.0862-0.0399-0.1513-0.13420.01760.33170.0785-0.00270.2395-0.00030.276937.586420.47547.6892
32.8518-0.20131.08392.3244-1.20471.9753-0.1195-0.04280.1397-0.02810.0551-0.3018-0.14650.02880.1050.35370.05280.00860.2435-0.04230.206243.001215.41067.1877
41.6346-0.1416-0.16860.7913-0.4840.8769-0.1071-0.09640.1207-0.00310.0997-0.01260.0706-0.00210.03270.36110.0559-0.00570.2799-0.02440.205746.87567.95349.5046
51.56310.50850.07254.2285-0.26951.0927-0.1341-0.36350.13550.23870.1060.0335-0.1195-0.07430.04890.36110.10650.01090.3577-0.03110.190341.86498.643421.9156
65.50623.66851.78693.85924.51238.3912-0.096-0.6185-0.03220.2239-0.0182-0.07790.18530.0390.05820.4520.17610.02590.47830.01010.197343.27022.56229.4911
73.28690.1472.61721.2192-0.09334.9409-0.2035-0.3790.26160.37670.21310.0039-0.1632-0.3564-0.01490.43950.14390.0290.381-0.06950.276732.668919.279223.7247
83.71552.8325-1.02272.4327-1.150.97060.0087-0.4102-0.05270.3804-0.11290.1348-0.1048-0.30470.1070.45620.1030.07870.4733-0.00030.253433.2040.784330.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 70 )A33 - 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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