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- PDB-6v83: Crystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase in... -

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Basic information

Entry
Database: PDB / ID: 6v83
TitleCrystal structure of CTX-M-14 E166A/P167S/D240G beta-lactamase in complex with ceftazidime-1
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
ACYLATED CEFTAZIDIME / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 Institute Of Allergy and Infectious Diseases (NIH/NIAID)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 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3442
Polymers27,8741
Non-polymers4691
Water4,179232
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)42.357, 42.357, 262.692
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-511-

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) / References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M PCB buffer pH 6, 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: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: DECTRIS PILATUS3 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: 1.8→41.82 Å / Num. obs: 23552 / % possible obs: 99.97 % / Redundancy: 16.7 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.024 / Rrim(I) all: 0.097 / Net I/σ(I): 31.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 2299 / CC1/2: 0.983 / Rpim(I) all: 0.137 / Rrim(I) all: 0.622 / % possible all: 100

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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: 1.8→41.82 Å / SU ML: 0.1605 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7365
RfactorNum. reflection% reflection
Rfree0.2074 1140 4.84 %
Rwork0.1713 --
obs0.173 23552 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 31 232 2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061991
X-RAY DIFFRACTIONf_angle_d0.9622712
X-RAY DIFFRACTIONf_chiral_restr0.0633321
X-RAY DIFFRACTIONf_plane_restr0.0059364
X-RAY DIFFRACTIONf_dihedral_angle_d6.1238303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.23641550.20282696X-RAY DIFFRACTION99.86
1.88-1.980.25071200.19812740X-RAY DIFFRACTION100
1.98-2.10.2671450.18712735X-RAY DIFFRACTION99.97
2.1-2.270.24161330.17892755X-RAY DIFFRACTION100
2.27-2.490.22561540.1812785X-RAY DIFFRACTION99.97
2.49-2.860.19961480.16962779X-RAY DIFFRACTION99.97
2.86-3.60.19141360.16592842X-RAY DIFFRACTION100
3.6-41.820.17161490.15463080X-RAY DIFFRACTION99.94
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)
10.785836066247-0.0565251140140.2385410353830.679375919569-0.002812879807980.6045135291360.00439744054978-0.02007874047260.04375441922380.05784342140190.002701846725630.06872904334350.00714116789408-0.0314391704751-0.001263741332230.1336968287130.0108096795949-0.01119431808270.08556855131850.007826471938750.112519683624-5.35604448285-7.4427152223417.8465376167
22.70656719753-2.570196720862.447116815754.66241326944-2.650600318244.53796955523-0.00754170271179-0.03930893005710.1043181487120.271419477213-0.0319687039191-0.0925840675869-0.1411807504180.04135160178930.02914163045080.133822194847-0.0167975630114-0.01158384323130.0702780124778-0.006161125330480.1135237386925.18684046625-2.6330134992623.0023635677
32.878538770680.7263757229731.063625819271.33546569616-0.2616920078572.04148619089-0.001469300010350.06092321033680.02936031946290.044576366104-0.0666528305572-0.118483668461-0.05596422890940.1354823133630.07084960095360.1237873390040.03363888982590.01723268647410.0736102058469-0.01383535337220.08104046472296.35119174157-8.0362193167415.2421694343
44.41563371796-0.0782557230993-0.9291813195554.82449540886-0.94468990693.785296718030.16576075801-0.276916803111-0.1906113639840.271522518304-0.05861750996120.1800716480690.205815545512-0.21188248729-0.09279671915670.152414183183-0.02561858963890.0139635758840.09906510900440.02049522271630.143402614958-11.8911684067-25.179704348723.2107889584
54.25347371178-0.2125475740420.5176259230333.446500211270.7743153387260.342978886670.00895785974891-0.00126796214066-0.1515579417440.08021392248290.00684746194258-0.2625543466430.1693569843920.0668409117818-0.03655511826840.1730157862860.01794623085150.002477975998270.0948597865885-0.01402201936260.09022018233495.0953521845-19.536421577314.3361618272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 195 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 194 )

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