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- PDB-8sj3: Beta-lactamase CTX-M-14 E166Y/N170G -

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Basic information

Entry
Database: PDB / ID: 8sj3
TitleBeta-lactamase CTX-M-14 E166Y/N170G
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE / beta-lactamase / enzyme / serine protease / antimicrobial resistance
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: 1.5 Å
AuthorsJudge, A. / Palzkill, T. / Sankaran, B. / Prasad, B.V.V. / Hu, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)32956 United States
CitationJournal: To Be Published
Title: Structure of CTX-M-14 E166Y/N170G at 1.5 Angstroms resolution
Authors: Judge, A. / Palkzill, T. / Sankaran, B. / Hu, L. / Prasad, B.V.V.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase CTX-M-14
B: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)55,9552
Polymers55,9552
Non-polymers00
Water9,116506
1
A: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)27,9781
Polymers27,9781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)27,9781
Polymers27,9781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.371, 42.371, 262.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Beta-lactamase CTX-M-14


Mass: 27977.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 20% w/v PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999889 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2021
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999889 Å / Relative weight: 1
ReflectionResolution: 1.5→32.97 Å / Num. obs: 70681 / % possible obs: 96 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.82 / Net I/σ(I): 3.26
Reflection shellResolution: 1.5→1.554 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 7283 / CC1/2: 0.487

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMv7.2.2data reduction
SCALAv3.3.8data scaling
PHASERv2.1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→32.97 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 3416 4.91 %
Rwork0.1424 66117 -
obs0.1452 69533 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 0 506 4397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584152
X-RAY DIFFRACTIONf_angle_d0.90675675
X-RAY DIFFRACTIONf_chiral_restr0.0743668
X-RAY DIFFRACTIONf_plane_restr0.0084747
X-RAY DIFFRACTIONf_dihedral_angle_d5.8334611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.26211270.17062399X-RAY DIFFRACTION83.26
1.52-1.540.24181250.15992596X-RAY DIFFRACTION88.89
1.54-1.570.25631470.14312782X-RAY DIFFRACTION94.3
1.57-1.590.2561610.14472753X-RAY DIFFRACTION97.17
1.59-1.620.21191390.1372914X-RAY DIFFRACTION98.8
1.62-1.650.21731550.13612852X-RAY DIFFRACTION99.47
1.65-1.680.23081540.1422890X-RAY DIFFRACTION99.09
1.68-1.720.22491490.14332861X-RAY DIFFRACTION98.59
1.72-1.750.29281180.14592951X-RAY DIFFRACTION98.9
1.75-1.790.22611350.14362809X-RAY DIFFRACTION98.59
1.79-1.840.25871590.13572888X-RAY DIFFRACTION97.82
1.84-1.890.20591540.12962760X-RAY DIFFRACTION97
1.89-1.950.21161620.12562810X-RAY DIFFRACTION96.68
1.95-2.010.2121330.12842831X-RAY DIFFRACTION96.05
2.01-2.080.19431340.13272752X-RAY DIFFRACTION95.5
2.08-2.160.1821140.13582788X-RAY DIFFRACTION94.84
2.16-2.260.20421330.13652736X-RAY DIFFRACTION94.13
2.26-2.380.21261080.1462729X-RAY DIFFRACTION92.17
2.38-2.530.19441710.14572668X-RAY DIFFRACTION93.02
2.53-2.720.20991500.14962642X-RAY DIFFRACTION90.97
2.72-30.16321500.15662643X-RAY DIFFRACTION90.36
3-3.430.17321250.14922602X-RAY DIFFRACTION90.03
3.43-4.320.18071440.13682616X-RAY DIFFRACTION89.61
4.32-32.970.16261690.14662845X-RAY DIFFRACTION97.83

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