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- PDB-7uon: CTX-M-14 Y105W mutant -

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Basic information

Entry
Database: PDB / ID: 7uon
TitleCTX-M-14 Y105W mutant
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJudge, A. / Hu, L. / Sankaran, B. / Van Riper, J. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI-32956 United States
CitationJournal: Commun Biol / Year: 2023
Title: Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M beta-lactamase.
Authors: Judge, A. / Hu, L. / Sankaran, B. / Van Riper, J. / Venkataram Prasad, B.V. / Palzkill, T.
History
DepositionApr 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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)28,1192
Polymers28,0241
Non-polymers951
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.430, 41.430, 230.641
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-618-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 28023.582 Da / Num. of mol.: 1 / Mutation: Y105W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 39.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES (0.1M), PEG 4,000 (25% 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 30, 2021
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.35→28.32 Å / Num. obs: 51539 / % possible obs: 99.1 % / Redundancy: 12.3 % / Biso Wilson estimate: 16.42 Å2 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Net I/σ(I): 17
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7337 / CC1/2: 0.961 / Rpim(I) all: 0.173 / Rrim(I) all: 0.58 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLM7.4.0data reduction
pointless1.11.17data scaling
PHASER2.1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.35→28.32 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 2519 4.9 %
Rwork0.2067 48889 -
obs0.2087 51408 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.65 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 5 252 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582034
X-RAY DIFFRACTIONf_angle_d0.84822783
X-RAY DIFFRACTIONf_chiral_restr0.0709330
X-RAY DIFFRACTIONf_plane_restr0.0052365
X-RAY DIFFRACTIONf_dihedral_angle_d11.8074298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.40531120.32832662X-RAY DIFFRACTION97.13
1.38-1.40.37751030.29772623X-RAY DIFFRACTION97.22
1.4-1.430.33381090.27542720X-RAY DIFFRACTION97.75
1.43-1.470.30891680.26342598X-RAY DIFFRACTION97.84
1.47-1.50.32481260.25852633X-RAY DIFFRACTION98.05
1.5-1.550.26341280.25172676X-RAY DIFFRACTION98.11
1.55-1.590.30381620.25692692X-RAY DIFFRACTION98.28
1.59-1.640.33851150.25282676X-RAY DIFFRACTION98.59
1.64-1.70.27151470.24322670X-RAY DIFFRACTION98.81
1.7-1.770.31671500.25422672X-RAY DIFFRACTION98.77
1.77-1.850.26971280.22912702X-RAY DIFFRACTION98.81
1.85-1.950.27191420.22822746X-RAY DIFFRACTION99.21
1.95-2.070.24711600.21282742X-RAY DIFFRACTION99.38
2.07-2.230.2391340.20512733X-RAY DIFFRACTION99.65
2.23-2.450.23961550.20672783X-RAY DIFFRACTION99.73
2.45-2.810.23681560.19212779X-RAY DIFFRACTION99.76
2.81-3.540.22351620.18162833X-RAY DIFFRACTION99.57
3.54-28.320.20531620.1732949X-RAY DIFFRACTION97.43

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