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- PDB-8pec: OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting S... -

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Basic information

Entry
Database: PDB / ID: 8pec
TitleOXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / Protein evolution. Antibiotic resistance. OXA-48. HYDROLASE. Serine-Beta-lactamase.
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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
Chem-CTJ / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7319
Polymers112,0114
Non-polymers1,7205
Water1,51384
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5904
Polymers56,0052
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1405
Polymers56,0052
Non-polymers1,1353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.147, 202.147, 55.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein
Beta-lactamase


Mass: 28002.713 Da / Num. of mol.: 4 / Mutation: A33V, K51E, F72L, S212A, T213A
Source method: isolated from a genetically manipulated source
Details: This is a A33V K51E F72L S212A T213A mutant / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CTJ / 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium


Mass: 549.600 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H25N6O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
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

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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 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.66→24.39 Å / Num. obs: 37514 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 73.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 9.1
Reflection shellResolution: 2.66→2.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.555 / Num. unique obs: 4578 / CC1/2: 0.367 / Rpim(I) all: 0.761 / Rrim(I) all: 1.846 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→24.39 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 1809 4.87 %
Rwork0.2023 35301 -
obs0.2055 37110 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.81 Å2
Refinement stepCycle: LAST / Resolution: 2.66→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 113 84 7669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857765
X-RAY DIFFRACTIONf_angle_d1.05310511
X-RAY DIFFRACTIONf_chiral_restr0.05511107
X-RAY DIFFRACTIONf_plane_restr0.00571343
X-RAY DIFFRACTIONf_dihedral_angle_d27.71822836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.730.37471270.3322468X-RAY DIFFRACTION90.54
2.73-2.810.34981570.30962608X-RAY DIFFRACTION96.38
2.81-2.90.38731560.30772681X-RAY DIFFRACTION98.92
2.9-3.010.34711440.29612723X-RAY DIFFRACTION99.48
3.01-3.130.36441400.28442737X-RAY DIFFRACTION99.07
3.13-3.270.31211340.26792748X-RAY DIFFRACTION99.76
3.27-3.440.25451440.22982734X-RAY DIFFRACTION99.65
3.44-3.650.29991350.2172732X-RAY DIFFRACTION99.34
3.66-3.940.25081630.19292732X-RAY DIFFRACTION99.38
3.94-4.330.2661190.18092755X-RAY DIFFRACTION98.66
4.33-4.950.23071040.15822794X-RAY DIFFRACTION99.38
4.95-6.220.2541280.19342778X-RAY DIFFRACTION98.11
6.22-24.390.23791580.16612811X-RAY DIFFRACTION98.18

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