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- PDB-5fao: CTX-M-15 in complex with FPI-1465 -

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Basic information

Entry
Database: PDB / ID: 5fao
TitleCTX-M-15 in complex with FPI-1465
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5VW / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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
Howard Hughes Medical Institute (HHMI) United States
Canadian Foundation For Innovation Canada
Canada Research Chairs Canada
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 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 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_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 30, 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)56,9824
Polymers56,2782
Non-polymers7052
Water59433
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4912
Polymers28,1391
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4912
Polymers28,1391
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.890, 62.730, 175.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 28138.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaUOE-1, bla, bla CTX-M-15, bla_1, bla_2, bla_3, blaCTX-M-15, blaCTX-M15, CTX-M-15, ECONIH1_02760, ECONIH1_27135, ERS085368_04262, ERS085370_01802, ERS085377_05268, ERS139214_01914, ERS139238_ ...Gene: blaUOE-1, bla, bla CTX-M-15, bla_1, bla_2, bla_3, blaCTX-M-15, blaCTX-M15, CTX-M-15, ECONIH1_02760, ECONIH1_27135, ERS085368_04262, ERS085370_01802, ERS085377_05268, ERS139214_01914, ERS139238_04648, ERS139238_04652, ERS150880_04508, HUS2011_pI0012, pCTXM15_EC8_00003, SK84_05077, SK86_03319
Production host: Escherichia coli (E. coli) / References: UniProt: Q9EXV5, beta-lactamase
#2: Chemical ChemComp-5VW / [[(3~{R},6~{S})-1-methanoyl-6-[[(3~{S})-pyrrolidin-3-yl]oxycarbamoyl]piperidin-3-yl]amino] hydrogen sulfate / FPI-1465, bound form


Mass: 352.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N4O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M MES pH6.5, 30% PEG5K monomethyl ether
PH range: 6.5

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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 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→33.28 Å / Num. obs: 10061 / % possible obs: 98.3 % / Redundancy: 4.4 % / Net I/σ(I): 7.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBT

4hbt


Resolution: 3.01→33.28 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.859 / SU B: 24.706 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27154 541 5.4 %RANDOM
Rwork0.22308 ---
obs0.22576 9487 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.233 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---0.31 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 3.01→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 46 33 3967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193994
X-RAY DIFFRACTIONr_bond_other_d0.0020.023894
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9795420
X-RAY DIFFRACTIONr_angle_other_deg2.22538948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9535516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.79724.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40915676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3981530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214546
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02850
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_it1.2212.7812076
X-RAY DIFFRACTIONr_mcbond_other1.2192.782075
X-RAY DIFFRACTIONr_mcangle_it1.8654.1462588
X-RAY DIFFRACTIONr_mcangle_other1.8664.1482589
X-RAY DIFFRACTIONr_scbond_it2.7373.2461918
X-RAY DIFFRACTIONr_scbond_other2.7363.2471919
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3074.6842833
X-RAY DIFFRACTIONr_long_range_B_refined5.55221.9093958
X-RAY DIFFRACTIONr_long_range_B_other5.55121.923959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.008→3.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 40 -
Rwork0.329 666 -
obs--96.45 %

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