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- PDB-6v6g: Crystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6v6g
TitleCrystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / drug resistance / protein evolution / protein structure / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 5, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0043
Polymers27,8741
Non-polymers1292
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.428, 41.428, 231.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21A-653-

HOH

31A-675-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27874.438 Da / Num. of mol.: 1
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M CaCl2, 0.1 M sodium acetate pH 5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.5→35.88 Å / Num. obs: 37871 / % possible obs: 98.84 % / Redundancy: 8.4 % / Biso Wilson estimate: 12.55 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.021 / Rrim(I) all: 0.06 / Net I/σ(I): 30.8
Reflection shellResolution: 1.5→1.56 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3494 / CC1/2: 0.96 / Rpim(I) all: 0.149 / Rrim(I) all: 0.488

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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: 1.5→35.88 Å / SU ML: 0.1432 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4508
RfactorNum. reflection% reflection
Rfree0.2171 1858 4.91 %
Rwork0.1827 --
obs0.1843 37871 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 8 280 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681965
X-RAY DIFFRACTIONf_angle_d0.91682670
X-RAY DIFFRACTIONf_chiral_restr0.0543317
X-RAY DIFFRACTIONf_plane_restr0.006350
X-RAY DIFFRACTIONf_dihedral_angle_d16.344282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.27831360.23062541X-RAY DIFFRACTION91.68
1.54-1.590.25941700.22792680X-RAY DIFFRACTION99.41
1.59-1.640.27111310.21432750X-RAY DIFFRACTION99.97
1.64-1.70.27641600.2192699X-RAY DIFFRACTION100
1.7-1.760.23641530.20882755X-RAY DIFFRACTION100
1.76-1.840.22121380.19822765X-RAY DIFFRACTION100
1.84-1.940.25181640.18962756X-RAY DIFFRACTION100
1.94-2.060.1961350.18522800X-RAY DIFFRACTION100
2.06-2.220.20831530.17552757X-RAY DIFFRACTION99.93
2.22-2.450.20851390.17662831X-RAY DIFFRACTION99.8
2.45-2.80.22951080.17352844X-RAY DIFFRACTION99.53
2.8-3.530.20451400.16692850X-RAY DIFFRACTION98.68
3.53-35.880.18091310.17022985X-RAY DIFFRACTION96.35
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)
11.347345470090.0597108253274-0.4116882056021.053107266530.2485023902831.646359531670.03962238688710.151070119513-0.233914278322-0.05084992371670.06127059077170.1951392986420.875212822005-0.181720739769-0.0413167890370.311935140254-0.027243075191-0.09292593854620.170402199557-0.01854375570890.1458011741541.71453034001-16.8891074576-27.1530314063
21.41633552055-0.100064156819-0.215301184650.3802604412020.3426491442910.7472495342250.0829976910833-0.367928987613-0.001797646218420.160567211574-0.03058451621670.06960374666930.0145109540665-0.5061757955450.3216367381940.0659453177081-0.0141762690512-0.0121156954880.3536759606070.02912436176650.124284143891-12.69908158471.26439827735-7.66632845678
32.474807680880.594580714060.9684791347574.175145818220.423153529362.83923138233-0.08685200342180.2098620047810.0752515978257-0.4862136272260.0422132052469-0.32112948326-0.3581662022960.1535399657450.120114219490.2995794396250.05328652368110.04925320218540.1781864342740.06452834064380.170809403104-3.4644041333315.9085011191-12.841583725
40.687107501543-0.424567322477-0.2933428125220.3939785586910.2898716616181.840850479780.05232764842890.199068935891-0.0377574178162-0.02063743367410.02755249449110.04906871710680.173002298243-0.432046931696-0.05749600131890.0501071571449-0.0457785722586-0.02882204486850.2239353913210.0224285239140.114203097256-5.95148436124-4.42427682822-17.709743207
54.531719908610.3651461421131.988328359132.073131127980.1778550424262.88611820532-0.03354129261930.2287562891720.2697848281-0.09960499232440.135640459603-0.01712023143480.1412414870840.3200855200690.01166927959110.105200590299-0.04130835515040.004431410092390.257272061761-0.03510213597950.06771683903174.52957731124-6.26349846031-31.8078039441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 289 )

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