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- PDB-8pea: OXA-48_F72L. Epistasis Arises from Shifting the Rate-Limiting Ste... -

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Basic information

Entry
Database: PDB / ID: 8pea
TitleOXA-48_F72L. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / Protein evolution. Antibiotic resistance. OXA-48.
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLeiros, H.-K.S. / Frohlich, C.
Funding support1items
OrganizationGrant numberCountry
Not funded0000
CitationJournal: Nat Catal / Year: 2024
Title: Epistasis arises from shifting the rate-limiting step during enzyme evolution of a beta-lactamase.
Authors: Frohlich, C. / Bunzel, H.A. / Buda, K. / Mulholland, A.J. / van der Kamp, M.W. / Johnsen, P.J. / Leiros, H.S. / Tokuriki, N.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)60,7613
Polymers60,7252
Non-polymers351
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.679, 82.823, 100.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 30362.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a F72L mutant / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris, pH 9.0 28-30% polyethylene glycol (PEG) mono ethylene ether 500 277 K. 10 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.97→44.41 Å / Num. obs: 38991 / % possible obs: 99.75 % / Redundancy: 7.1 % / Biso Wilson estimate: 37.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1072 / Rpim(I) all: 0.04355 / Rrim(I) all: 0.1159 / Net I/σ(I): 19.05
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 3822 / CC1/2: 0.898 / Rpim(I) all: 0.5769 / Rrim(I) all: 1.474 / % possible all: 99.74

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→25 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 3048 4.13 %
Rwork0.2043 70693 -
obs0.206 38958 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.74 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 1 295 4244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914067
X-RAY DIFFRACTIONf_angle_d1.18335509
X-RAY DIFFRACTIONf_chiral_restr0.0694582
X-RAY DIFFRACTIONf_plane_restr0.0103709
X-RAY DIFFRACTIONf_dihedral_angle_d17.64981487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.42071360.38493184X-RAY DIFFRACTION99.16
2-2.030.39091410.39053193X-RAY DIFFRACTION99.67
2.03-2.070.37731460.34443249X-RAY DIFFRACTION99.59
2.07-2.110.38531380.31233236X-RAY DIFFRACTION99.68
2.11-2.150.37911370.29583187X-RAY DIFFRACTION99.67
2.15-2.190.28841350.28753226X-RAY DIFFRACTION99.82
2.19-2.240.30721380.26733212X-RAY DIFFRACTION99.17
2.24-2.290.30131400.26623201X-RAY DIFFRACTION99.73
2.29-2.350.30841420.25793222X-RAY DIFFRACTION99.47
2.35-2.410.3021400.25783208X-RAY DIFFRACTION99.94
2.41-2.480.33831410.23683226X-RAY DIFFRACTION99.88
2.48-2.560.31941400.23463261X-RAY DIFFRACTION99.94
2.56-2.650.35721400.23213192X-RAY DIFFRACTION99.88
2.65-2.760.2681340.22593221X-RAY DIFFRACTION99.91
2.76-2.890.25091430.22853217X-RAY DIFFRACTION99.73
2.89-3.040.32111350.22123213X-RAY DIFFRACTION99.47
3.04-3.230.26021380.21873200X-RAY DIFFRACTION98.93
3.23-3.480.25931350.18533220X-RAY DIFFRACTION99.58
3.48-3.830.18481390.17483225X-RAY DIFFRACTION99.67
3.83-4.380.20111430.153227X-RAY DIFFRACTION99.7
4.38-5.520.17691360.14643184X-RAY DIFFRACTION99.1
5.52-250.16931310.16493189X-RAY DIFFRACTION98.63

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