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- PDB-8ela: CTX-M-14 beta-lactamase mutant - N132A w MES -

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Basic information

Entry
Database: PDB / ID: 8ela
TitleCTX-M-14 beta-lactamase mutant - N132A w MES
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase antibiotic beta-lactam
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLu, S. / Palzkill, T. / Hu, L. / 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: 2023
Title: Mutagenesis and structural analysis reveal the CTX-M beta-lactamase active site is optimized for cephalosporin catalysis and drug resistance.
Authors: Lu, S. / Montoya, M. / Hu, L. / Neetu, N. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69910
Polymers55,9152
Non-polymers7848
Water11,295627
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3505
Polymers27,9581
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3505
Polymers27,9581
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.314, 60.430, 264.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21A-727-

HOH

31B-521-

HOH

41B-632-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27957.520 Da / Num. of mol.: 2 / Mutation: N132A
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
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9L5C7, beta-lactamase

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Non-polymers , 5 types, 635 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01 M Zinc chloride, 0.1 M MES, PEG 6,000 (20% w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 69335 / % possible obs: 76 % / Redundancy: 5.9 % / Biso Wilson estimate: 12.62 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.039 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6 / Num. unique obs: 10897 / CC1/2: 0.916 / Rpim(I) all: 0.06 / % possible all: 90.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.5→29.66 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 2846 4.96 %
Rwork0.1731 54532 -
obs0.1749 57378 75.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.57 Å2 / Biso mean: 15.8836 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.5→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 38 627 4557
Biso mean--18.18 25.07 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.24971590.20122825298479
1.53-1.550.22541540.19273152330688
1.55-1.580.25251540.19343168332288
1.58-1.620.24221600.18813084324486
1.62-1.650.2311730.18743071324486
1.65-1.690.22861810.18323047322885
1.69-1.730.22591320.1863004313684
1.73-1.780.20941680.1862936310481
1.78-1.830.23011450.17792879302480
1.83-1.890.2451580.1732776293478
1.89-1.960.23371510.18172690284175
1.96-2.040.24461200.17572702282274
2.04-2.130.22731380.17142545268370
2.13-2.240.19791180.16872494261269
2.24-2.380.20131150.17032377249266
2.38-2.570.21061200.17642319243964
2.57-2.820.20261340.17222145227959
2.82-3.230.19911150.1712103221858
3.23-4.070.1531950.1542145224058
4.07-29.660.18921560.16323070322679

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