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- PDB-8dpq: Beta-lactamase CTX-M-14 N170A -

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Basic information

Entry
Database: PDB / ID: 8dpq
TitleBeta-lactamase CTX-M-14 N170A
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / Antibiotic resistance / Beta-lactam / CTX-M-14
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsLu, S. / Neetu, N. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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
DepositionJul 15, 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9543
Polymers27,8291
Non-polymers1242
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.418, 41.418, 230.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

21A-645-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27829.393 Da / Num. of mol.: 1 / Mutation: N170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium HEPES pH7.5, 25% (w/v) PEG 8000

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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: Feb 28, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.67→35.4 Å / Num. obs: 27171 / % possible obs: 97.31 % / Redundancy: 9.1 % / Biso Wilson estimate: 12.98 Å2 / Rrim(I) all: 0.071 / Net I/σ(I): 9
Reflection shellResolution: 1.671→1.73 Å / Num. unique obs: 2567 / Rrim(I) all: 0.18

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.67→35.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.256 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23292 1406 5.2 %RANDOM
Rwork0.17055 ---
obs0.17383 25763 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.67→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 8 280 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191997
X-RAY DIFFRACTIONr_bond_other_d0.0030.021886
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9682714
X-RAY DIFFRACTIONr_angle_other_deg1.20534371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27324.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91115328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7361515
X-RAY DIFFRACTIONr_chiral_restr0.1410.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212237
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02374
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5351.8091047
X-RAY DIFFRACTIONr_mcbond_other3.52952.7421046
X-RAY DIFFRACTIONr_mcangle_it3.9832.7071306
X-RAY DIFFRACTIONr_mcangle_other3.9816.3581307
X-RAY DIFFRACTIONr_scbond_it4.3632.164950
X-RAY DIFFRACTIONr_scbond_other4.3612.164950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7933.1331408
X-RAY DIFFRACTIONr_long_range_B_refined5.50412474
X-RAY DIFFRACTIONr_long_range_B_other5.50512475
X-RAY DIFFRACTIONr_rigid_bond_restr5.6231991
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded24.48951961
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 94 -
Rwork0.2 1815 -
obs--93.58 %

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