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- PDB-6i5d: Crystal structure of an OXA-48 beta-lactamase synthetic mutant -

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Basic information

Entry
Database: PDB / ID: 6i5d
TitleCrystal structure of an OXA-48 beta-lactamase synthetic mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-48 MUTANT / ANTIBIOTIC
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZavala, A. / Retailleau, P. / Dabos, L. / Naas, T. / Iorga, B.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-33 France
French National Research AgencyANR-14-JAMR-0002 France
CitationJournal: To be published
Title: Substrate specificity of an OXA-48 beta-lactamase synthetic mutant
Authors: Dabos, L. / Zavala, A. / Dortet, L. / Bonnin, R.A. / Beckstein, O. / Retailleau, P. / Iorga, B.I. / Naas, T.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,96634
Polymers59,5392
Non-polymers2,42632
Water6,774376
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint30 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.571, 92.984, 126.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 29769.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3729690_05506
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 7 types, 408 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaNO3; 20% PEG3350 protein stored at 12.5mg/ml in buffer: Sodium Phosphate 0.1M pH=7.0; K2SO4 50mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.75→74.9 Å / Num. obs: 58856 / % possible obs: 97.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.035 / Rrim(I) all: 0.056 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2944 / CC1/2: 0.849 / Rpim(I) all: 0.368 / Rrim(I) all: 0.575 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20160617data reduction
Aimless0.5.29data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2894 4.97 %RANDOM
Rwork0.17 ---
obs0.171 58275 97.5 %-
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1--8.7899 Å20 Å20 Å2
2--2.7494 Å20 Å2
3---6.0404 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.75→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 155 376 4520
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014377HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965901HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1597SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes641HARMONIC5
X-RAY DIFFRACTIONt_it4377HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion540SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5384SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2326 220 5.1 %
Rwork0.2195 4091 -
all0.2202 4311 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71020.11960.32731.11150.38951.75450.01410.00640.01790.0310.0037-0.0216-0.05540.0891-0.0177-0.0506-0.00920.007-0.0775-0.013-0.0556-12.04657.0607-22.8043
20.99520.0676-0.04061.10960.00811.3052-0.05410.0330.0175-0.14980.1038-0.1339-0.06070.1917-0.0497-0.0587-0.02230.0267-0.0468-0.0289-0.0658-7.258-7.9068-50.9727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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