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- PDB-8peb: OXA-48_Q5. Epistasis Arises from Shifting the Rate-Limiting Step ... -

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Basic information

Entry
Database: PDB / ID: 8peb
TitleOXA-48_Q5. 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 / plasma membrane
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
MALONATE ION / DI(HYDROXYETHYL)ETHER / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4137
Polymers28,0031
Non-polymers4116
Water6,341352
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,82714
Polymers56,0052
Non-polymers82112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4600 Å2
ΔGint-113 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.401, 42.544, 64.304
Angle α, β, γ (deg.)90.000, 106.875, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-301-

CL

21A-729-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28002.713 Da / Num. of mol.: 1 / Mutation: A33V K51E F72L S212A T213A
Source method: isolated from a genetically manipulated source
Details: This is a mutant with these changes: A33V K51E F72L S212A T213A
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21AI harboring modified pURR expression
References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 358 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris, pH 9.0 (Sigma-Aldrich) 28-30% polyethylene glycol (PEG) mono ethylene ether 500 (Sigma-Aldrich)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.17→24.95 Å / Num. obs: 82172 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 4 % / Rmerge(I) obs: 0.798 / Num. unique obs: 4063 / CC1/2: 0.521 / Rpim(I) all: 0.615 / Rrim(I) all: 1.244 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→24.95 Å / SU ML: 0.1284 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1872 1248 1.52 %
Rwork0.1647 80910 -
obs0.1651 82158 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 1.17→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 22 352 2350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912273
X-RAY DIFFRACTIONf_angle_d1.16353109
X-RAY DIFFRACTIONf_chiral_restr0.0867320
X-RAY DIFFRACTIONf_plane_restr0.0073416
X-RAY DIFFRACTIONf_dihedral_angle_d18.7139844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.220.2971280.3058951X-RAY DIFFRACTION99.86
1.22-1.270.2781500.27368928X-RAY DIFFRACTION99.75
1.27-1.340.26951330.23828979X-RAY DIFFRACTION99.95
1.34-1.420.24191480.21558985X-RAY DIFFRACTION99.97
1.42-1.530.20171380.1898975X-RAY DIFFRACTION99.97
1.53-1.690.18361260.16789028X-RAY DIFFRACTION99.92
1.69-1.930.19551390.16129033X-RAY DIFFRACTION99.81
1.93-2.430.19631420.15358932X-RAY DIFFRACTION98.99
2.43-24.950.1541440.13969099X-RAY DIFFRACTION98.58

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