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- PDB-6qw8: Crystal structure of CTX-M-15 complexed with relebactam (16 hour soak) -

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Basic information

Entry
Database: PDB / ID: 6qw8
TitleCrystal structure of CTX-M-15 complexed with relebactam (16 hour soak)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / inhibitor / relebactam / diazabicyclooctane / antibiotic resistance.
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
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-MK7 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam.
Authors: Tooke, C.L. / Hinchliffe, P. / Lang, P.A. / Mulholland, A.J. / Brem, J. / Schofield, C.J. / Spencer, J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 9, 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: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0246
Polymers28,2931
Non-polymers7315
Water6,630368
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-8 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.538, 45.563, 117.915
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: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Solu
References: UniProt: G3G192, UniProt: W1EPV7*PLUS, beta-lactamase
#2: Chemical ChemComp-MK7 / (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide / MK-7655, bound form


Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→44.54 Å / Num. obs: 97874 / % possible obs: 99.7 % / Redundancy: 11.9 % / Rpim(I) all: 0.029 / Net I/σ(I): 19.3
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 5.9 / Num. unique obs: 4521 / Rpim(I) all: 0.145

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBT

4hbt


Resolution: 1.1→42.5 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 9.78
RfactorNum. reflection% reflection
Rfree0.1313 5057 5.17 %
Rwork0.1147 --
obs0.1156 97784 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 44 368 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142124
X-RAY DIFFRACTIONf_angle_d1.4612890
X-RAY DIFFRACTIONf_dihedral_angle_d20.99805
X-RAY DIFFRACTIONf_chiral_restr0.097331
X-RAY DIFFRACTIONf_plane_restr0.021376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.15261600.13892855X-RAY DIFFRACTION93
1.1125-1.12560.13931720.13192932X-RAY DIFFRACTION97
1.1256-1.13930.14021710.13043050X-RAY DIFFRACTION99
1.1393-1.15380.13181620.12243016X-RAY DIFFRACTION99
1.1538-1.16890.1351950.11883057X-RAY DIFFRACTION100
1.1689-1.18490.12221470.11723068X-RAY DIFFRACTION100
1.1849-1.20190.12941950.11723073X-RAY DIFFRACTION100
1.2019-1.21980.1271730.10993038X-RAY DIFFRACTION100
1.2198-1.23890.12941680.10963088X-RAY DIFFRACTION100
1.2389-1.25920.12211350.10763067X-RAY DIFFRACTION100
1.2592-1.28090.12771910.10643061X-RAY DIFFRACTION100
1.2809-1.30420.12221700.10693096X-RAY DIFFRACTION100
1.3042-1.32930.11461790.10843059X-RAY DIFFRACTION100
1.3293-1.35640.14151690.10713108X-RAY DIFFRACTION100
1.3564-1.38590.12791450.10693085X-RAY DIFFRACTION100
1.3859-1.41820.12411710.09893071X-RAY DIFFRACTION100
1.4182-1.45360.10831760.09593072X-RAY DIFFRACTION100
1.4536-1.49290.12541610.09553104X-RAY DIFFRACTION100
1.4929-1.53690.13071730.09463113X-RAY DIFFRACTION100
1.5369-1.58650.1121760.09333074X-RAY DIFFRACTION100
1.5865-1.64320.11411420.09283130X-RAY DIFFRACTION100
1.6432-1.7090.12041250.09933148X-RAY DIFFRACTION100
1.709-1.78670.11141880.10063098X-RAY DIFFRACTION100
1.7867-1.88090.11961810.10553106X-RAY DIFFRACTION100
1.8809-1.99880.11581650.10143138X-RAY DIFFRACTION100
1.9988-2.15310.11951560.10043128X-RAY DIFFRACTION100
2.1531-2.36980.1271480.11013182X-RAY DIFFRACTION100
2.3698-2.71260.13022030.11593137X-RAY DIFFRACTION100
2.7126-3.41740.14821640.13493227X-RAY DIFFRACTION100
3.4174-42.53220.15951960.14793346X-RAY DIFFRACTION100

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