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- PDB-5fa7: CTX-M-15 in complex with FPI-1523 -

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Basic information

Entry
Database: PDB / ID: 5fa7
TitleCTX-M-15 in complex with FPI-1523
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-5VR / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 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 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Nov 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

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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)57,6214
Polymers56,9722
Non-polymers6492
Water9,368520
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8112
Polymers28,4861
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8112
Polymers28,4861
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.730, 60.270, 76.010
Angle α, β, γ (deg.)90.00, 112.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase /


Mass: 28486.230 Da / Num. of mol.: 2 / Fragment: residues 26-291
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-5VR / [[(3~{R},6~{S})-6-(acetamidocarbamoyl)-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate


Mass: 324.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N4O7S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→70.1 Å / Num. obs: 59836 / % possible obs: 98.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.67 Å2 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.67→33.4 Å / Cor.coef. Fo:Fc: 0.9385 / Cor.coef. Fo:Fc free: 0.9203 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 3068 5.13 %RANDOM
Rwork0.175 ---
obs0.1767 59810 98.39 %-
Displacement parametersBiso mean: 16.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.7967 Å20 Å2-1.4902 Å2
2---0.6746 Å20 Å2
3---2.4713 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: 1 / Resolution: 1.67→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7846 0 42 520 8408
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017976HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1214448HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1181HARMONIC5
X-RAY DIFFRACTIONt_it7976HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion14.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion553SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9204SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2506 218 4.95 %
Rwork0.2081 4184 -
all0.2102 4402 -
obs--98.39 %
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)
10.2923-0.07190.03180.24120.01780.6122-0.0249-0.0076-0.0060.00430.0003-0.02090.0140.02150.0246-0.07030.0017-0.0365-0.0012-0.00010.004216.6607-3.435718.2839
20.39540.0794-0.03460.2389-0.00720.62430.00020.0362-0.0014-0.00970.0263-0.0056-0.0349-0.0133-0.0265-0.07310.0083-0.0406-0.01250.00580.007115.3338-8.9331-18.4739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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