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- PDB-7uht: SSX Structure of Metallo Beta-Lactamase L1 with One Zinc in the A... -

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Basic information

Entry
Database: PDB / ID: 7uht
TitleSSX Structure of Metallo Beta-Lactamase L1 with One Zinc in the Active Site
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
Biological speciesStenotrophomonas maltophilia K279a (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. / Srajer, V. / 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
DepositionMar 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Oct 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)29,3092
Polymers29,2441
Non-polymers651
Water81145
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)117,2378
Polymers116,9764
Non-polymers2624
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 area9200 Å2
ΔGint-193 kcal/mol
Surface area39730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.094, 106.094, 99.772
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

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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 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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
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: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→46.84 Å / Num. obs: 17389 / % possible obs: 100 % / Redundancy: 54.3 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.91 / R split: 0.277 / Net I/σ(I): 2.99
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 861 / R split: 0.82
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 / Support base: xyz stage
Serial crystallography data reductionCrystal hits: 3374 / Frames indexed: 2947 / Frames total: 18000 / Lattices indexed: 2947

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Processing

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

7l52


Resolution: 2.2→46.84 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 827 4.76 %
Rwork0.2145 16556 -
obs0.2164 17383 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 1 45 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022036
X-RAY DIFFRACTIONf_angle_d0.52972782
X-RAY DIFFRACTIONf_chiral_restr0.0394312
X-RAY DIFFRACTIONf_plane_restr0.0036366
X-RAY DIFFRACTIONf_dihedral_angle_d17.1153725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.35341400.3272683X-RAY DIFFRACTION99.93
2.34-2.520.31341340.30352708X-RAY DIFFRACTION99.96
2.52-2.770.30721220.26962716X-RAY DIFFRACTION99.96
2.77-3.170.34411330.23912741X-RAY DIFFRACTION100
3.17-40.23951380.18182775X-RAY DIFFRACTION99.97
4-46.840.18191600.16092933X-RAY DIFFRACTION99.97
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)
11.932556920461.274415035421.217051218052.89448251893-0.9901720409423.08085763276-0.4337518231050.133265617313-0.159281181365-0.8043184302210.05058295597120.1698997109340.328333190961-0.2895557904720.3587880492280.7090746344840.126041572630.08464359576920.67764360629-0.004197930553810.5380373910029.1872284134423.743317292213.9470894584
23.30368109567-1.32696235078-0.1918438035843.83763503968-0.07233011463594.94065966516-0.131397556316-0.455247531984-0.7644568676640.004682646404180.03198270154720.503940020880.5094357615810.1008746955230.06131850531880.3850315512050.08415893951730.07252341183140.2497137905610.02122185205690.36469918007535.278593197617.44604937013.85056468974
32.27982400898-0.566900633228-0.8522663521632.483308578820.0846205641692.67599088523-0.0181024499778-0.0435688855638-0.1316172201040.1963720861-0.00578330246845-0.2847397961250.3083636783660.2510451583850.01237093548120.2517800286610.0450279957932-0.01933206884560.2316363803570.008386534252970.29603265365739.949834305425.054820986610.8550270515
40.725999333553-0.1685727782090.1896330002591.430581101750.06637240857421.1338436847-0.0566423338675-0.020466579967-0.0553065120219-0.00283655264438-0.09280061721990.02447012896920.0528600769778-0.03273065464980.1362602116790.2013467551320.028983470390.01560614267540.23041179312-0.01683799412390.16337516117330.061495832835.73684825827.03530634368
52.71533563522-0.3823918562921.085026636112.07353431249-0.03446196182692.10848164457-0.1288208840330.0856220188015-0.553861990266-0.310933058321-0.0711269049280.009148959564030.1805295825040.2485771462410.1768519447210.2672735324490.06624713149990.07122177148650.2694791106010.02899556394870.35658313006138.266741629429.4156728827-5.34293563653
64.22483448711-2.23727497072-0.7056429387884.796671468840.7224016421990.739319350434-0.11450034698-0.367312394858-0.0554154975504-0.1964008449970.1380679416210.305232055261-0.15176754778-0.00495037923956-0.007850546152370.2669703755370.0541808414246-0.06499836803590.324510544637-0.06064875990950.32678135047315.274695446436.5606512229-5.40261477964
72.163138772730.379578820798-0.1818253862610.2055816846920.514616294022.88985159455-0.01297688531830.241009997262-0.134312361791-0.235389069398-0.081615956898-0.04031579806540.2344871947380.07798082349710.1000646147490.2878572120930.05915486525090.001578893975550.24465808783-0.04297648930080.32728892316430.512079978225.0730136374-9.20731425595
87.804901976-2.005981629291.36371295163.2898289234-0.1936635666472.316136585760.477494827088-0.2095350472090.243437985356-0.24002093019-0.3376280620980.07884497082840.357397388469-0.346966959839-0.1227956381090.4446840664630.0109193619315-0.02246301736830.328660222908-0.09876947616210.28493532638817.707022640628.6059595639-14.6349078842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 204 )
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 222 )
7X-RAY DIFFRACTION7chain 'A' and (resid 223 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 287 )

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