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- PDB-7k2x: Crystal structure of CTX-M-14 E166A/K234R Beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 7k2x
TitleCrystal structure of CTX-M-14 E166A/K234R Beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / CTX-M-14
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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Feb 10, 2021Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1May 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 2.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 2.3Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
E: Beta-lactamase
F: Beta-lactamase
G: Beta-lactamase
H: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,39312
Polymers221,0258
Non-polymers3684
Water27,8691547
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7202
Polymers27,6281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7202
Polymers27,6281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7202
Polymers27,6281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7202
Polymers27,6281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.373, 83.373, 232.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Beta-lactamase


Mass: 27628.133 Da / Num. of mol.: 8 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1547 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl, 0.1 M Tris-Cl, pH 8.0, 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: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.8→45.23 Å / Num. obs: 2042053 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.31 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→4.88 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 166864

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Processing

Software
NameVersionClassification
PHENIXdev_3386refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.8→45.23 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 8348 5.02 %
Rwork0.1814 157917 -
obs0.1836 166265 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15524 0 0 1547 17071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007515752
X-RAY DIFFRACTIONf_angle_d0.904121439
X-RAY DIFFRACTIONf_chiral_restr0.05382544
X-RAY DIFFRACTIONf_plane_restr0.00562823
X-RAY DIFFRACTIONf_dihedral_angle_d8.91289591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.25673780.23095164X-RAY DIFFRACTION99.46
1.82-1.840.2832900.22395301X-RAY DIFFRACTION99.86
1.84-1.870.2333130.19275170X-RAY DIFFRACTION99.82
1.87-1.890.25433160.2025238X-RAY DIFFRACTION99.91
1.89-1.910.26932780.25312X-RAY DIFFRACTION99.96
1.91-1.940.24152640.19525349X-RAY DIFFRACTION99.86
1.94-1.970.24992420.19055264X-RAY DIFFRACTION99.91
1.97-20.23553140.18775239X-RAY DIFFRACTION99.95
2-2.030.24122590.19155303X-RAY DIFFRACTION99.91
2.03-2.060.23822740.17795232X-RAY DIFFRACTION99.95
2.06-2.10.24042530.17515301X-RAY DIFFRACTION99.95
2.1-2.140.20972920.16775373X-RAY DIFFRACTION99.89
2.14-2.180.22782640.17035165X-RAY DIFFRACTION99.89
2.18-2.220.22922400.17485388X-RAY DIFFRACTION99.98
2.22-2.270.23942600.185291X-RAY DIFFRACTION99.93
2.27-2.320.22822180.18165364X-RAY DIFFRACTION99.96
2.32-2.380.22893000.17425221X-RAY DIFFRACTION99.84
2.38-2.450.23632020.18295360X-RAY DIFFRACTION99.93
2.45-2.520.23132820.17565279X-RAY DIFFRACTION99.96
2.52-2.60.20762990.17475289X-RAY DIFFRACTION99.93
2.6-2.690.22952920.1815261X-RAY DIFFRACTION99.96
2.69-2.80.25772330.18075256X-RAY DIFFRACTION99.85
2.8-2.930.20422230.1745297X-RAY DIFFRACTION99.93
2.93-3.080.1942660.17245393X-RAY DIFFRACTION99.75
3.08-3.270.20932860.17325204X-RAY DIFFRACTION99.71
3.27-3.530.19542170.16865326X-RAY DIFFRACTION99.64
3.53-3.880.19813100.17925172X-RAY DIFFRACTION98.94
3.88-4.440.21133540.17445170X-RAY DIFFRACTION99.48
4.44-5.590.23063370.1815237X-RAY DIFFRACTION99.46
5.59-45.20.23262920.21664998X-RAY DIFFRACTION95.47

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