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- PDB-5wi3: Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D b... -

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Basic information

Entry
Database: PDB / ID: 5wi3
TitleStructure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to cefotaxime
ComponentsOXA-239
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter sp. enrichment culture clone 8407 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHarper, T.M. / June, C.M. / Powers, R.A. / Leonard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI082416 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489 United States
CitationJournal: Biochem. J. / Year: 2018
Title: Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239.
Authors: Harper, T.M. / June, C.M. / Taracila, M.A. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Sep 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_host_org_strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 2023Group: 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 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: OXA-239
A: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3674
Polymers57,5722
Non-polymers7952
Water4,161231
1
B: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1842
Polymers28,7861
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1842
Polymers28,7861
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.095, 143.032, 44.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 31 - 273 / Label seq-ID: 11 - 253

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein OXA-239


Mass: 28786.166 Da / Num. of mol.: 2 / Mutation: K82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. enrichment culture clone 8407 (environmental samples)
Gene: OXA-239 / Variant: K82D / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YCI1, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07814 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07814 Å / Relative weight: 1
ReflectionResolution: 1.81→98.1 Å / Num. obs: 57689 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.046 / Net I/σ(I): 13.1
Reflection shellResolution: 1.811→1.817 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 542 / CC1/2: 0.873 / Rpim(I) all: 0.505 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0X

4k0x


Resolution: 1.81→80.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.389 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20458 2827 4.9 %RANDOM
Rwork0.17993 ---
obs0.18115 54798 99.75 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.969 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.81→80.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 52 231 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193925
X-RAY DIFFRACTIONr_bond_other_d0.0020.023605
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9635332
X-RAY DIFFRACTIONr_angle_other_deg1.00338350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9225.795176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44715676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.21514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
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_it2.6672.3311951
X-RAY DIFFRACTIONr_mcbond_other2.6592.331950
X-RAY DIFFRACTIONr_mcangle_it3.7163.4742443
X-RAY DIFFRACTIONr_mcangle_other3.723.4752444
X-RAY DIFFRACTIONr_scbond_it3.8822.7011974
X-RAY DIFFRACTIONr_scbond_other3.8812.7041975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8523.9182885
X-RAY DIFFRACTIONr_long_range_B_refined8.19829.0294424
X-RAY DIFFRACTIONr_long_range_B_other8.19729.0364425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14926 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 212 -
Rwork0.331 4007 -
obs--100 %
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)
11.8817-0.3253-0.41986.02750.17451.7863-0.0657-0.1289-0.1656-0.2923-0.08720.13090.12010.08740.15290.0388-0.01020.01450.06820.03210.0959-24.1872.557-11.908
23.30910.1201-0.75571.54360.32221.85670.0519-0.10050.11180.130.0251-0.0663-0.09790.2215-0.07690.0266-0.0058-0.01590.0447-0.01620.043-8.28334.006-0.068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B31 - 273
2X-RAY DIFFRACTION2A31 - 273

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