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- PDB-7k2y: Crystal structure of CTX-M-14 E166A/K234R Beta-lactamase in compl... -

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Basic information

Entry
Database: PDB / ID: 7k2y
TitleCrystal structure of CTX-M-14 E166A/K234R Beta-lactamase in complex with hydrolyzed ampicillin
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / acyl-enzyme intermediate
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Chem-AIX / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLu, S. / Palzkill, T. / Sankaran, B. / Hu, L. / Soeung, V. / Prasad, B.V.V.
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: A drug-resistant beta-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency.
Authors: Soeung, V. / Lu, S. / Hu, L. / Judge, A. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Oct 18, 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)28,0812
Polymers27,7291
Non-polymers3511
Water4,288238
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 area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.630, 41.630, 231.473
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-610-

HOH

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Components

#1: Protein Beta-lactamase /


Mass: 27729.236 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2H4FY00, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium Chloride 0.1 M HEPES pH7 20%(w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.62→30.6 Å / Num. obs: 56337 / % possible obs: 98.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 17.46 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 18
Reflection shellResolution: 1.62→5.12 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 30633 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.62→30.6 Å / SU ML: 0.1858 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 22.5979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 2807 4.98 %
Rwork0.1876 53530 -
obs0.1895 56337 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.48 Å2
Refinement stepCycle: LAST / Resolution: 1.62→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 24 238 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551999
X-RAY DIFFRACTIONf_angle_d0.81132724
X-RAY DIFFRACTIONf_chiral_restr0.0479324
X-RAY DIFFRACTIONf_plane_restr0.0055363
X-RAY DIFFRACTIONf_dihedral_angle_d6.09641221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.35221540.25832658X-RAY DIFFRACTION98.05
1.65-1.680.31371420.25282650X-RAY DIFFRACTION97.79
1.68-1.710.3226920.24232660X-RAY DIFFRACTION98.22
1.71-1.750.24191600.23822722X-RAY DIFFRACTION98.36
1.75-1.780.25581640.2342600X-RAY DIFFRACTION98.4
1.78-1.820.26931140.22422679X-RAY DIFFRACTION98.48
1.82-1.870.26751460.21852684X-RAY DIFFRACTION98.5
1.87-1.920.22531620.2192613X-RAY DIFFRACTION98.75
1.92-1.980.29831520.20972727X-RAY DIFFRACTION98.97
1.98-2.040.24141800.2072596X-RAY DIFFRACTION98.97
2.04-2.110.29431180.20822750X-RAY DIFFRACTION99.07
2.11-2.20.211520.2062677X-RAY DIFFRACTION99.3
2.2-2.30.22971210.19372726X-RAY DIFFRACTION99.44
2.3-2.420.25591530.20022661X-RAY DIFFRACTION99.4
2.42-2.570.2881980.19942744X-RAY DIFFRACTION99.54
2.57-2.770.25151080.19122763X-RAY DIFFRACTION99.72
2.77-3.050.20731170.18012667X-RAY DIFFRACTION99.36
3.05-3.490.21841670.16962711X-RAY DIFFRACTION99.86
3.49-4.390.16331380.14392675X-RAY DIFFRACTION99.58
4.39-30.60.18771690.15722567X-RAY DIFFRACTION95.33
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)
14.03255385361-0.4047386254112.012979704461.579083306170.04870677219413.56308491469-0.1056835873670.1630737746220.401407024004-0.16142252277-0.0554816010532-0.0995388906891-1.002632466870.1985900586830.2171736985630.322238372986-0.02009799625510.0262937825560.2042446525210.0292191026770.151284142526-3.7047247795116.8288188582-31.4187204945
22.77520588571-0.9595241098321.612874404581.23897901838-0.4079362984252.71994824662-0.0791806604864-0.043463777690.2121223751680.0417494689958-0.0299856387516-0.131437166355-0.7011607213170.5660910029260.07961359482370.164685939673-0.06831592394290.02118629205370.332976557951-0.006843240842160.1585489571645.0029542927110.593337153-16.4861261742
31.538645191040.02040115374430.8260083990640.05488756918240.1719941066541.0189821130.200432246287-0.111346027222-0.285199475827-0.147680024786-0.187749817949-0.1640956356190.4156872954820.68387258315-0.3754281334490.4060164121840.287085063847-0.1029203513990.615366197417-0.02847966302880.26076454544212.4281924402-10.241941777-5.05673342294
41.15624386211-0.422837960021-0.2307678323470.216284348073-0.2833634497272.332986816850.231346113530.170984367837-0.188546725091-0.264430481012-0.166353854834-0.003325283130260.5042323942180.783842672099-0.03204641107350.2438073648670.183048691678-0.0387987043220.291252364621-0.05379664963240.1743116931736.05290429481-6.19211584387-11.4432121404
51.67820848976-0.5476754350030.03190361691121.0045059517-0.7040914528631.89287630839-0.01463735470450.1436480205890.175900027170.1349017387970.0323867941404-0.0744956488026-0.3809632730050.720192542483-0.05266362040670.115997144424-0.0948291677741-0.0178448212350.4027253555880.00752227241670.1450023270024.910769329697.48683481578-14.2236891563
61.24859661974-1.396533179430.1282477791741.631298238860.238522043551.787949361830.2059406997430.3807265702120.0731221722404-0.228968164897-0.0563294459304-0.256864068414-0.1045016773520.8482583470690.3295884623260.0123271092940.003018187044190.0407184679160.6286754088660.01289245704590.1555989741746.249112393436.08503540131-27.7145802148
78.50961240931.60830963715-1.693303809034.20539277330.02107387104583.9281755396-0.1362685796180.40788311486-0.425917227599-0.3241915282750.213707416079-0.01663434448950.00314057569899-0.140102619927-0.0783701334380.106122222848-0.00428360132175-0.04101439478180.280951200180.01746455052060.110224931864-4.595731851656.22061200583-31.8391511766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 212 )
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 289 )

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