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- PDB-5oe0: CRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-181 -

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Basic information

Entry
Database: PDB / ID: 5oe0
TitleCRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-181
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / antibiotic resistance / oxacillinase / OXA-48-like / carbapenemase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05000841209 Å
AuthorsLund, B.A. / Carlsen, T.J.O. / Leiros, H.K.S. / Thomassen, A.M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis.
Authors: Lund, B.A. / Thomassen, A.M. / Carlsen, T.J.O. / Leiros, H.K.S.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 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

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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)60,9194
Polymers60,7872
Non-polymers1322
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The homolog OXA-48 form dimers in solution, supported by SEC. Our DSC results with OXA-181 and OXA-48 indicate that OXA-181 is also a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.927, 143.927, 53.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 24 - 265

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and ((resid 24 and (name N or name...AA
22chain 'B'BB

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Components

#1: Protein Beta-lactamase


Mass: 30393.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-181 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G5CKK8, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0, 0.2M Ammonium sulfate 20.5 % PEG MME 5000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.05→35.98175 Å / Num. obs: 40027 / % possible obs: 99.55 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.6502174613 Å2 / Rrim(I) all: 0.08461 / Net I/σ(I): 13.19
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.27 / Num. measured obs: 26225 / Num. unique obs: 3911 / Rrim(I) all: 0.8693 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtk

5dtk


Resolution: 2.05000841209→35.98175 Å / SU ML: 0.300132202378 / Cross valid method: FREE R-VALUE / σ(F): 1.34986800148 / Phase error: 28.5063987825
RfactorNum. reflection% reflectionSelection details
Rfree0.242015913009 1971 4.94517901498 %Random selection
Rwork0.201511357357 ---
obs0.203524764137 39857 99.5752866815 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.7569216215 Å2
Refinement stepCycle: LAST / Resolution: 2.05000841209→35.98175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 6 476 4438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002759367172514058
X-RAY DIFFRACTIONf_angle_d0.5368568315895493
X-RAY DIFFRACTIONf_chiral_restr0.0432579851114576
X-RAY DIFFRACTIONf_plane_restr0.00308736927255707
X-RAY DIFFRACTIONf_dihedral_angle_d19.31868767252383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.4251011791111320.3547010560252677X-RAY DIFFRACTION99.1178546224
2.1013-2.15810.3552610173591260.3267817598522670X-RAY DIFFRACTION99.2193044713
2.1581-2.22160.3539395466671290.3010844702962719X-RAY DIFFRACTION99.3719469644
2.2216-2.29330.3177977099951170.304710707452680X-RAY DIFFRACTION99.1843971631
2.2933-2.37520.2675664571811290.2630623430322689X-RAY DIFFRACTION99.4705259442
2.3752-2.47030.3052281832711330.2509970652282711X-RAY DIFFRACTION99.5449772489
2.4703-2.58270.2757749329071460.2367618255552679X-RAY DIFFRACTION99.5770179767
2.5827-2.71880.2645023344651730.2354886830112666X-RAY DIFFRACTION99.7190024587
2.7188-2.88910.2861374771871280.2110074496162727X-RAY DIFFRACTION99.5814440181
2.8891-3.1120.2414414208941550.2154334862552680X-RAY DIFFRACTION99.7888067582
3.112-3.4250.225158060071430.1761922817722713X-RAY DIFFRACTION99.8252359315
3.425-3.92010.2252818611621500.1544054948192725X-RAY DIFFRACTION99.9652294854
3.9201-4.93690.1710968531171830.1355000583592714X-RAY DIFFRACTION100
4.9369-35.98730.2119886756881270.173024981942836X-RAY DIFFRACTION99.7979117548
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)
11.580574998010.0250774924038-0.07206461437652.274218526830.07388347625870.9827600020790.001444225428480.06117266045970.01191776708110.0695957425268-0.06705350123220.3850925242480.0694883173563-0.06504455725890.05487731779440.222313878732-0.02858289104790.009349363476460.2291147509780.03001131583680.275177522131-51.104029094140.737402583914.4485324437
22.577905600350.633170183253-0.1236470391241.96917963759-0.08873045030381.325156281230.0773986175145-0.228209424432-0.3632837578380.202685272066-0.0469357228836-0.411384006070.09351381478440.106293669475-0.01284313327450.2084707409310.00593204079326-0.06762230179610.1968491143020.03577678928140.28924255338-18.629393943739.366893898417.5150099346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)

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