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

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Basic information

Entry
Database: PDB / ID: 5wib
TitleStructure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem
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
Imipenem / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter sp. enrichment culture clone 8407 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 19, 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 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,1754
Polymers57,5722
Non-polymers6032
Water4,071226
1
A: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0882
Polymers28,7861
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0882
Polymers28,7861
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.398, 144.744, 43.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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, barbiturase
#2: Chemical ChemComp-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.868→81.38 Å / Num. obs: 53055 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.7
Reflection shellResolution: 1.868→1.875 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 504 / CC1/2: 0.781 / % possible all: 100

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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: 1.87→81.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.32 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22843 2613 4.9 %RANDOM
Rwork0.18582 ---
obs0.18792 50364 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.32 Å20 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 1.87→81.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 35 226 4004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193875
X-RAY DIFFRACTIONr_bond_other_d00.023569
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9595256
X-RAY DIFFRACTIONr_angle_other_deg0.66438280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8375484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8125.795176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62915673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6231514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.020.024317
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02745
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_it3.0172.5631933
X-RAY DIFFRACTIONr_mcbond_other3.0172.5631932
X-RAY DIFFRACTIONr_mcangle_it4.0593.8262415
X-RAY DIFFRACTIONr_mcangle_other4.0583.8262416
X-RAY DIFFRACTIONr_scbond_it3.7932.8311942
X-RAY DIFFRACTIONr_scbond_other3.7942.8281940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3794.1262841
X-RAY DIFFRACTIONr_long_range_B_refined7.61431.4444499
X-RAY DIFFRACTIONr_long_range_B_other7.5431.0514459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.868→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 198 -
Rwork0.331 3686 -
obs--99.64 %
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)
13.9505-0.2566-0.16121.5439-0.39241.7503-0.04630.36960.126-0.22930.09680.1444-0.0515-0.1469-0.05060.0813-0.0564-0.03130.20510.0130.02388.28734.90844.021
21.32290.7772-0.41816.0077-0.69231.58950.0338-0.0883-0.14670.3429-0.2039-0.0130.04990.07840.17010.0625-0.01560.03770.1992-0.0270.057723.8052.78954.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 273
2X-RAY DIFFRACTION2B30 - 273

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