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- PDB-7ass: OXA-48_L67F_CAZ. What Doesnt Kill You Makes You Stronger: Sub-MIC... -

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Basic information

Entry
Database: PDB / ID: 7ass
TitleOXA-48_L67F_CAZ. What Doesnt Kill You Makes You Stronger: Sub-MIC Selection Drives Cryptic Evolution of OXA-48
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / OXA-48 / ceftazidime / resistance development / cryptic evolution / Escherichia coli / carbapenemase / carbapenem / collateral sensitivity / sub-MIC
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
hydrolyzed ceftazidime / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFrohlich, C. / Leiros, H.-K.S.
CitationJournal: Msphere / Year: 2021
Title: Cryptic beta-Lactamase Evolution Is Driven by Low beta-Lactam Concentrations.
Authors: Frohlich, C. / Gama, J.A. / Harms, K. / Hirvonen, V.H.A. / Lund, B.A. / van der Kamp, M.W. / Johnsen, P.J. / Samuelsen, O. / Leiros, H.S.
History
DepositionOct 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)123,20311
Polymers121,8954
Non-polymers1,3087
Water14,358797
1
A: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6196
Polymers60,9472
Non-polymers6724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-28 kcal/mol
Surface area20380 Å2
MethodPISA
2
B: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5845
Polymers60,9472
Non-polymers6373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-19 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.555, 108.476, 125.423
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: 30473.740 Da / Num. of mol.: 4 / Mutation: L67F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_3, blaOXA-48, B6R99_29845, G5637_27540, GJJ01_28680, KPE71T_00045, SAMEA3649466_05396, SAMEA3673128_05462, SAMEA3729780_05587
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-RYE / hydrolyzed ceftazidime / (2R)-2-[(1R)-1-[[(2Z)-2-(2-azanyl-1,3-thiazol-4-yl)-2-(2-methyl-1-oxidanyl-1-oxidanylidene-propan-2-yl)oxyimino-ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5-(pyridin-1-ium-1-ylmethyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 565.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N6O8S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 9.0, 28-30% PEG mono ethylene ether 500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 94247 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.099 / Net I/σ(I): 9.6
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4653 / CC1/2: 0.583 / Rpim(I) all: 1.11

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5QB4

5qb4


Resolution: 1.91→23.56 Å / SU ML: 0.2345 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7395 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 4702 5 %
Rwork0.1873 89271 -
obs0.1894 93973 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.33 Å2
Refinement stepCycle: LAST / Resolution: 1.91→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 81 797 8822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01078370
X-RAY DIFFRACTIONf_angle_d1.028211358
X-RAY DIFFRACTIONf_chiral_restr0.05641178
X-RAY DIFFRACTIONf_plane_restr0.00671470
X-RAY DIFFRACTIONf_dihedral_angle_d25.3623050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.34971700.33152944X-RAY DIFFRACTION99.78
1.93-1.950.30531650.30852939X-RAY DIFFRACTION99.68
1.95-1.980.31611740.28712895X-RAY DIFFRACTION99.71
1.98-20.3431530.2772960X-RAY DIFFRACTION99.97
2-2.030.30941610.27382937X-RAY DIFFRACTION99.9
2.03-2.060.30511290.262984X-RAY DIFFRACTION99.87
2.06-2.090.2721590.24742936X-RAY DIFFRACTION99.74
2.09-2.120.26131480.23342937X-RAY DIFFRACTION99.87
2.12-2.150.3011630.22742956X-RAY DIFFRACTION99.87
2.15-2.190.24991470.22012938X-RAY DIFFRACTION99.58
2.19-2.220.27721580.20742950X-RAY DIFFRACTION99.74
2.22-2.260.23981600.20832946X-RAY DIFFRACTION99.81
2.26-2.310.29531560.20822956X-RAY DIFFRACTION99.9
2.31-2.350.24721540.19842948X-RAY DIFFRACTION99.65
2.35-2.410.2981370.20212966X-RAY DIFFRACTION99.74
2.41-2.460.24891550.19042973X-RAY DIFFRACTION99.71
2.46-2.520.25131600.18072970X-RAY DIFFRACTION99.97
2.52-2.590.2441750.17582930X-RAY DIFFRACTION99.81
2.59-2.670.30741510.18952955X-RAY DIFFRACTION99.81
2.67-2.750.23141740.18342948X-RAY DIFFRACTION99.74
2.75-2.850.23041440.17813013X-RAY DIFFRACTION99.91
2.85-2.970.24221450.18392968X-RAY DIFFRACTION99.97
2.97-3.10.20581410.17543022X-RAY DIFFRACTION99.87
3.1-3.260.22691470.18743013X-RAY DIFFRACTION99.97
3.26-3.470.23471550.16892963X-RAY DIFFRACTION99.68
3.47-3.730.19081520.163028X-RAY DIFFRACTION99.97
3.73-4.110.18781700.1433012X-RAY DIFFRACTION100
4.11-4.70.16621610.13413035X-RAY DIFFRACTION99.97
4.7-5.90.17461630.14943080X-RAY DIFFRACTION99.91
5.9-23.560.18591750.19283169X-RAY DIFFRACTION99.49

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