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- PDB-6v5e: Crystal structure of CTX-M-14 P167S/D240G beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6v5e
TitleCrystal structure of CTX-M-14 P167S/D240G beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / drug resistance / protein evolution / conformational change / enzyme kinetics / enzyme catalysis / protein stability / protein-drug interaction
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrown, C.A. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI32956 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Antagonism between substitutions in beta-lactamase explains a path not taken in the evolution of bacterial drug resistance.
Authors: Brown, C.A. / Hu, L. / Sun, Z. / Patel, M.P. / Singh, S. / Porter, J.R. / Sankaran, B. / Prasad, B.V.V. / Bowman, G.R. / Palzkill, T.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9931
Polymers27,9931
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.237, 42.237, 261.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27993.297 Da / Num. of mol.: 1 / Mutation: P167S, D240G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BET08_34355, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON66_01305, BON69_22545, BON71_04040, BON75_10525, BON76_14325, BON81_01055, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BXT93_06855, C5N07_28500, C5P43_21980, CDL37_21060, CR538_26855, CRT46_23505, DW236_20870, EIA08_25160, EIA21_26975, ELT23_05930, ETN48_p0088, FNJ69_13810, FQR64_24895, FTV90_03295, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4370290_00046
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C7, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB Buffer pH 4.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7 Å / Num. obs: 10104 / % possible obs: 88.28 % / Redundancy: 7 % / Biso Wilson estimate: 29.57 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.121 / Num. unique obs: 880 / CC1/2: 0.978 / Rpim(I) all: 0.046 / Rrim(I) all: 0.13

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 2.3→41.7 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 474 4.69 %
Rwork0.1854 9630 -
obs0.1883 10104 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 124 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291991
X-RAY DIFFRACTIONf_angle_d0.68482709
X-RAY DIFFRACTIONf_chiral_restr0.0456322
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d16.3325283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.29851600.20973011X-RAY DIFFRACTION86.05
2.63-3.320.29411640.20873154X-RAY DIFFRACTION88.65
3.32-41.70.21081500.16733465X-RAY DIFFRACTION90.08
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)
15.807261865870.6221125662962.613408812424.198482414861.00971871985.08442725414-0.001335112253180.1989119584870.301747856937-0.0703431290494-0.19318357605-0.445341591272-0.3329523447010.6629632848110.089334016550.278230398848-0.008675226020290.04497282134280.2228278766920.02815057773540.27693992993634.212530645121.791787430118.8691797943
20.6502775151320.3799925827170.2611032101571.31753145961-0.1699329788060.5942485653460.03090893991020.0247884306479-0.02277621199360.003253530226440.005449007837480.02572570693750.105890632925-0.0286835089263-0.02636061558330.2283200790510.01881653010340.01645455742630.233418530802-0.001405858190340.21478129473917.98429985274.5851520768317.4895087249
32.13641239957-1.580727470691.676885612642.74933754182-1.87035756733.131446042770.026842497947-0.187940083171-0.03939765987760.3026328628080.05063853274590.1275690563880.1770138113160.0189833364761-0.09846689643570.304106850823-0.0426517481839-0.03042100233670.211164417590.01089383545210.19295042669126.688712334915.632244612322.9509001716
43.65090292428-0.5306529071590.6819451065276.93211400656-4.358704118157.949453484750.12965894972-0.1501098387310.206895287-0.151609973506-0.1568019403240.069501128449-0.574664514225-0.328660631610.02489562599450.3018661184840.0133950033264-0.04074001396060.161227517687-0.03359507162770.18658414496126.039519520723.70649614722.7839640486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 290 )

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