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- PDB-5fap: CTX-M-15 in complex with FPI-1602 -

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Basic information

Entry
Database: PDB / ID: 5fap
TitleCTX-M-15 in complex with FPI-1602
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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-602 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Canadian Foundation for Innovation Canada
Canada research Chair Programs 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 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: 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 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0084
Polymers56,2782
Non-polymers7312
Water1,53185
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5042
Polymers28,1391
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5042
Polymers28,1391
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.120, 61.830, 73.070
Angle α, β, γ (deg.)90.00, 103.98, 90.00
Int Tables number4
Space group name H-MP1211

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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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M MES pH6.5, 30% PEG5K monomethyl ether

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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: 2.7→30.97 Å / Num. obs: 14478 / % possible obs: 95.4 % / Redundancy: 2.5 % / Net I/σ(I): 11.7

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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: 2.7→30.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 761 5.3 %RANDOM
Rwork0.187 ---
obs0.189 13713 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.13 Å2
2--0.46 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 48 85 4011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193986
X-RAY DIFFRACTIONr_bond_other_d00.023884
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9745410
X-RAY DIFFRACTIONr_angle_other_deg3.87938924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44224.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67415676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0481530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214550
X-RAY DIFFRACTIONr_gen_planes_other0.010.02848
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_it2.042.6082068
X-RAY DIFFRACTIONr_mcbond_other2.0412.6082067
X-RAY DIFFRACTIONr_mcangle_it3.1823.9092578
X-RAY DIFFRACTIONr_mcangle_other3.1813.9092579
X-RAY DIFFRACTIONr_scbond_it2.6742.9071918
X-RAY DIFFRACTIONr_scbond_other2.6732.9071919
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2974.2412829
X-RAY DIFFRACTIONr_long_range_B_refined5.48720.2984126
X-RAY DIFFRACTIONr_long_range_B_other5.48620.3024122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 59 -
Rwork0.27 964 -
obs--92.25 %

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