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- PDB-7l91: Structure of Metallo Beta-Lactamase L1 in a Complex with Hydrolyz... -

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Basic information

Entry
Database: PDB / ID: 7l91
TitleStructure of Metallo Beta-Lactamase L1 in a Complex with Hydrolyzed Moxalactam Determined by Pink-Beam Serial Crystallography
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / metallo beta lactamase / moxalactam / serial crystallography / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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-XQP / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Henning, R. / Maltseva, N. / Endres, M. / Babnigg, G. / Vukica, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase.
Authors: Wilamowski, M. / Sherrell, D.A. / Kim, Y. / Lavens, A. / Henning, R.W. / Lazarski, K. / Shigemoto, A. / Endres, M. / Maltseva, N. / Babnigg, G. / Burdette, S.C. / Srajer, V. / Joachimiak, A.
History
DepositionJan 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 16, 2022Group: Database references / Polymer sequence / Category: entity_poly / pdbx_database_related / Item: _entity_poly.pdbx_target_identifier
Revision 2.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9134
Polymers29,2441
Non-polymers6693
Water1,27971
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,65316
Polymers116,9764
Non-polymers2,67712
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 area9040 Å2
ΔGint-46 kcal/mol
Surface area38660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.853, 105.853, 99.100
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)
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-434-

HOH

21A-471-

HOH

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Components

#1: Protein Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)


Mass: 29243.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XQP / (2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid


Mass: 538.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N6O10S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 7816

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 289 K / Method: batch mode
Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate ...Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350.

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.18
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Feb 11, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.181
ReflectionResolution: 2.2→33.03 Å / Num. obs: 14754 / % possible obs: 86.42 % / Redundancy: 35.4 % / Biso Wilson estimate: 22.15 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 30.51
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 15.96 / Num. unique obs: 1143
Serial crystallography sample deliveryDescription: Nylon Mesh / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: ALEX mesh holder
Motion control: SmarAct Motors viaPMAC start/stop raster over area
Sample holding: nylon mesh
Sample solvent: buffer 0.0075 Tris, 0.05 M KCl, 0.75 mM TCEP, 2.5 mM ZnCl2, 0.075 M sodium malonate pH 8.0, 10% (w/v) PEG3350
Support base: xyz stage
Serial crystallography data reductionCrystal hits: 7816 / Frames indexed: 583 / Frames total: 19316

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOLREPphasing
Precognitiondata reduction
Epinormdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L52

7l52


Resolution: 2.2→33.03 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.7205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 773 5.25 %
Rwork0.1814 13950 -
obs0.1827 14723 85.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 39 71 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032075
X-RAY DIFFRACTIONf_angle_d0.62672838
X-RAY DIFFRACTIONf_chiral_restr0.0416315
X-RAY DIFFRACTIONf_plane_restr0.0042374
X-RAY DIFFRACTIONf_dihedral_angle_d19.0325753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.2216870.2031546X-RAY DIFFRACTION58.53
2.34-2.520.23381150.22782109X-RAY DIFFRACTION79.51
2.52-2.770.27471300.22972347X-RAY DIFFRACTION88.09
2.77-3.170.23971510.21522497X-RAY DIFFRACTION93.27
3.17-40.20121150.16472654X-RAY DIFFRACTION96.31
4-33.030.1661750.14152797X-RAY DIFFRACTION97.06
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)
10.8842476994290.4780306773510.7072183810494.472710691432.963658024672.67880921031-0.0698200795917-0.1615049795160.2835313985280.131461188954-0.1224344650150.628268717533-0.12907919698-0.3624347796280.1976257019850.1824580269090.04473751388450.01351429545910.1478045753370.02267776864880.16311306246130.450886296613.52435714639.49503885883
21.20955156991-0.664457032007-0.08667260360243.43691223134-0.1110523506731.99054886681-0.01787690099860.06579830292730.0767924172519-0.177405785875-0.0654247970845-0.0630284086637-0.0797954097192-0.04790717717440.06159134223160.1266865971090.0035262582183-0.01403392146990.129547771379-0.01563667370130.14278859464542.384320694513.88673251176.55505421446
31.0654802023-0.1463416739980.213514610991.424795088580.04401158081030.933898337071-0.1176525356450.01907797322570.2100698596010.163941113688-0.0431472728342-0.0261171151425-0.18767582117-0.0383802215440.1076884650510.210773969340.0469258023955-0.03347471011660.0872691233907-0.005373299530380.20971966672547.251069540914.536229427117.0511009909
44.31760715171.238596255480.6484565040727.74825594961-0.8320720568721.17719392105-0.05328105487890.209704668875-0.3616026564070.2355266112740.1033998257890.653665037272-0.0866907911869-0.0585617358125-0.04773709004670.25934009181-0.005637598239980.05065942081580.09601498209970.01361033538230.23887174347139.2729220568-4.9821166373121.8939986813
58.386841040574.94367913431.873285081215.415222835841.135052181610.443033117921-0.390864584048-0.321700232246-0.1604432807350.4471142260440.3132236859050.04106244417860.5028969468890.06287134237580.1274028849710.3736437960080.06842253516930.01609693787060.130341485831-0.0004433720166050.16024544661143.57259487922.2137842507829.0451813172
61.0643248840.3233117140910.1874940387074.568964167320.005687995444182.16732318920.0995420415179-0.2410207524130.4693309725270.0003585450399340.1148199194840.0688621638052-0.516314052197-0.314623845107-0.2118563601330.2934662729040.09512832881950.02564007390860.2030820413-0.03249806211640.29242275543233.570086770419.632494783123.9651668128
76.335881729740.0822920122726-1.355948438124.82897955803-0.8901021726357.04839380927-0.311481003217-0.215519337633-0.1956632766540.7835407382980.3266350877540.3519671064590.363316245766-0.5287223281490.01913995172930.2988801842710.08576509743910.07700256495750.302864994114-0.009294645832660.17510507288233.6911500851.2494098518931.1335949447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 235 )
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 287 )

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