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- PDB-6hoo: Crystal Structure of Rationally Designed OXA-48loop18 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6hoo
TitleCrystal Structure of Rationally Designed OXA-48loop18 beta-lactamase
ComponentsBeta-lactamase,OXA-48loop18,Beta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-48loop18 / ANTIBIOTIC
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / Beta-lactamase / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZavala, A. / Retailleau, P. / Dabos, L. / Naas, T. / Iorga, B.
Funding support France, 1items
OrganizationGrant numberCountry
ANR-10-LABX-33 France
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Substrate Specificity of OXA-48 after beta 5-beta 6 Loop Replacement.
Authors: Dabos, L. / Zavala, A. / Bonnin, R.A. / Beckstein, O. / Retailleau, P. / Iorga, B.I. / Naas, T.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 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

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Assembly

Deposited unit
A: Beta-lactamase,OXA-48loop18,Beta-lactamase
B: Beta-lactamase,OXA-48loop18,Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41621
Polymers57,7032
Non-polymers1,71219
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-124 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.650, 126.650, 126.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-310-

F

21B-428-

HOH

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Components

#1: Protein Beta-lactamase,OXA-48loop18,Beta-lactamase


Mass: 28851.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-244, blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A023ZTE5, UniProt: A0A0U4UUJ9, UniProt: Q6XEC0*PLUS, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate; 0.2 M ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.38→44.78 Å / Num. obs: 27195 / % possible obs: 99.7 % / Redundancy: 16.2 % / Biso Wilson estimate: 57.457 Å2 / Rrim(I) all: 0.146 / Net I/av σ(I): 0.999 / Net I/σ(I): 16.69
Reflection shellResolution: 2.38→2.53 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 4273 / CC1/2: 0.582 / Rrim(I) all: 1.84 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSVERSION Jan 26, 2018data reduction
Aimless0.6.2data scaling
MrBUMP00.9.00phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2K

4s2k


Resolution: 2.38→19.78 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1357 5 %RANDOM
Rwork0.171 ---
obs0.173 27144 99.3 %-
Displacement parametersBiso max: 181.78 Å2 / Biso mean: 61.14 Å2 / Biso min: 31.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.38→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 100 103 4268
Biso mean--71.42 56.41 -
Num. residues----502
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1494SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it4267HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion526SEMIHARMONIC5
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_contact5209SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4267HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5759HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion18.09
LS refinement shellResolution: 2.38→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2245 131 4.98 %
Rwork0.216 2498 -
all0.2164 2629 -
obs--93 %
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)
11.3574-0.86340.03292.5030.03521.0709-0.02320.0370.16280.1510.0194-0.1873-0.13490.1690.0037-0.026-0.0394-0.0308-0.16020.027-0.025111.5685-11.3835-27.4083
21.0747-0.1296-0.08791.7015-0.17531.6693-0.02150.268-0.1115-0.2394-0.1510.1910.0642-0.24140.1725-0.03690.0176-0.0389-0.0865-0.1008-0.0282-6.8627-33.9783-44.3014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|3 - B|251 }B3 - 251
2X-RAY DIFFRACTION2{ A|3 - A|251 }A3 - 251

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