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- PDB-5fat: OXA-48 in complex with FPI-1602 -

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Basic information

Entry
Database: PDB / ID: 5fat
TitleOXA-48 in complex with FPI-1602
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
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
Chem-602 / : / : / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKing, A.M. / King, D.T. / French, S. / Brouillette, E. / Asli, A. / Alexander, A.N. / Vuckovic, M. / Maiti, S.N. / Parr, T.R. / Brown, E.D. ...King, A.M. / King, D.T. / French, S. / Brouillette, E. / Asli, A. / Alexander, A.N. / Vuckovic, M. / Maiti, S.N. / Parr, T.R. / Brown, E.D. / Malouin, F. / Strynadka, N.C.J. / Wright, G.D.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Canada Research Chair Programs Canada
Canadian Foundation for Innovation Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural and Kinetic Characterization of Diazabicyclooctanes as Dual Inhibitors of Both Serine-beta-Lactamases and Penicillin-Binding Proteins.
Authors: King, A.M. / King, D.T. / French, S. / Brouillette, E. / Asli, A. / Alexander, J.A. / Vuckovic, M. / Maiti, S.N. / Parr, T.R. / Brown, E.D. / Malouin, F. / Strynadka, N.C. / Wright, G.D.
History
DepositionDec 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_conn_angle ...pdbx_audit_support / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 13, 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
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,83015
Polymers56,3682
Non-polymers1,46213
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-51 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.110, 75.750, 106.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 28183.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-602 / [[(3~{R},6~{S})-6-[(azetidin-3-ylcarbonylamino)carbamoyl]-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate


Mass: 365.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O7S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005 M CoCl2, 0.005 M CdCl2, 0.005 M MgCl2, 0.005 M NiCl2, 0.1 M HEPES pH 7.5, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→47.18 Å / Num. obs: 35720 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.09→47.18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.547 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1851 5.2 %RANDOM
Rwork0.1671 ---
obs0.16956 33810 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.494 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å20 Å2
2--2.5 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.09→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 59 295 4332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194132
X-RAY DIFFRACTIONr_bond_other_d0.0010.023890
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9225586
X-RAY DIFFRACTIONr_angle_other_deg0.76938918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79124.476210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4091524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
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_it3.1873.2571948
X-RAY DIFFRACTIONr_mcbond_other3.173.2551947
X-RAY DIFFRACTIONr_mcangle_it4.0584.862428
X-RAY DIFFRACTIONr_mcangle_other4.0584.862429
X-RAY DIFFRACTIONr_scbond_it4.4663.6692184
X-RAY DIFFRACTIONr_scbond_other4.4653.6712185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.165.3483155
X-RAY DIFFRACTIONr_long_range_B_refined7.59727.3335206
X-RAY DIFFRACTIONr_long_range_B_other7.55127.085072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 169 -
Rwork0.216 2417 -
obs--99.88 %

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