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- PDB-6hb8: Crystal structure of OXA-517 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6hb8
TitleCrystal structure of OXA-517 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
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
2-ETHOXYETHANOL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRaczynska, J.E. / Dabos, L. / Zavala, A. / Retailleau, P. / Iorga, B. / Jaskolski, M. / Naas, T.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-33 France
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant.
Authors: Dabos, L. / Raczynska, J.E. / Bogaerts, P. / Zavala, A. / Girlich, D. / Bonnin, R.A. / Dortet, L. / Peyrat, A. / Retailleau, P. / Iorga, B.I. / Jaskolski, M. / Glupczynski, Y. / Naas, T.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Sep 9, 2026Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)120,82130
Polymers118,5584
Non-polymers2,26326
Water13,241735
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,21913
Polymers59,2792
Non-polymers94011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-73 kcal/mol
Surface area20300 Å2
MethodPISA
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,60217
Polymers59,2792
Non-polymers1,32315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-124 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.800, 125.046, 82.656
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA22 - 2653 - 244
21ALAALAPROPROBB22 - 2653 - 244
12VALVALPHEPHEAA21 - 2662 - 245
22VALVALPHEPHECC21 - 2662 - 245
13GLUGLUPROPROAA24 - 2655 - 244
23GLUGLUPROPRODD24 - 2655 - 244
14ALAALAPROPROBB22 - 2653 - 244
24ALAALAPROPROCC22 - 2653 - 244
15GLUGLUPROPROBB24 - 2655 - 244
25GLUGLUPROPRODD24 - 2655 - 244
16GLUGLUPROPROCC24 - 2655 - 244
26GLUGLUPROPRODD24 - 2655 - 244

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 29639.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Plasmid: pET41b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U8YI81, beta-lactamase

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Non-polymers , 6 types, 761 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5 and 20% (w/v) PEG10000 / PH range: 293

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980104506016 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980104506016 Å / Relative weight: 1
ReflectionResolution: 1.86→46.18 Å / Num. obs: 84548 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.16 / Net I/σ(I): 6.8
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 13554 / CC1/2: 0.35 / Rrim(I) all: 1.25 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s2p

4s2p


Resolution: 1.86→46.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.644 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21885 4277 5.1 %RANDOM
Rwork0.17003 ---
obs0.17246 80268 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å20.01 Å2
2---0.95 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.86→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 131 735 8818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0148435
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177469
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.66111406
X-RAY DIFFRACTIONr_angle_other_deg0.9611.6617508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43422.795483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.328151473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.961551
X-RAY DIFFRACTIONr_chiral_restr0.0770.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021671
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8093.7383915
X-RAY DIFFRACTIONr_mcbond_other3.8073.7373914
X-RAY DIFFRACTIONr_mcangle_it4.7425.5944893
X-RAY DIFFRACTIONr_mcangle_other4.7415.5954894
X-RAY DIFFRACTIONr_scbond_it5.2794.2384520
X-RAY DIFFRACTIONr_scbond_other5.2774.2384520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1346.1536498
X-RAY DIFFRACTIONr_long_range_B_refined8.29344.4410100
X-RAY DIFFRACTIONr_long_range_B_other8.29344.43910100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87280.06
12B87280.06
21A88170.05
22C88170.05
31A86860.06
32D86860.06
41B88370.06
42C88370.06
51B88590.05
52D88590.05
61C87820.06
62D87820.06
LS refinement shellResolution: 1.857→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 293 -
Rwork0.339 5895 -
obs--99.04 %

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