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- PDB-8ehh: Crystal structure of the class A extended-spectrum beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 8ehh
TitleCrystal structure of the class A extended-spectrum beta-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase inhibitor / DBO / ESBL / ceftazidimase
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/transpeptidase-like
Similarity search - Domain/homology
Chem-MK7 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsPower, P. / Ghiglione, B. / Bonomo, R.A. / Rodriguez, M.M. / Gutkind, G. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National Scientific and Technical Research Council (CONICET)11220200100191CO Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2018-01550 Argentina
CitationJournal: To be published
Title: Biochemical and structural evidences of the activity of relebactam as inhibitor of the extended-spectrum beta-lactamase CTX-M-96.
Authors: Ghiglione, B. / Rodriguez, M.M. / Gutkind, G. / Bonomo, R.A. / Klinke, S. / Power, P.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / entity / pdbx_contact_author / pdbx_database_related / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details ..._entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle
Description: Missing anisotropic B-factor
Details: The actual reason for replacement was a request by one of the reviewers of the submitted manuscript requesting that, due to the high resolution of the structure, anisotropic B-factors and ...Details: The actual reason for replacement was a request by one of the reviewers of the submitted manuscript requesting that, due to the high resolution of the structure, anisotropic B-factors and hydrogen atoms have to be included in the structure. We agreed with that. A revised manuscript with the updated coordinates will be submitted soon for publication.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4762
Polymers28,1261
Non-polymers3501
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.480, 45.590, 117.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 28125.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-12 variant, blaCTX-M / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ZXB6, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42 % / Description: rectangular prisms
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.9 / Details: 1.55 M sodium chloride + 1.55 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.885601 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2021
Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885601 Å / Relative weight: 1
ReflectionResolution: 1.03→42.51 Å / Num. obs: 117183 / % possible obs: 98.5 % / Redundancy: 11.7 % / Biso Wilson estimate: 9.57 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.05 / Net I/σ(I): 30.09
Reflection shellResolution: 1.03→1.067 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 7 / Num. unique obs: 17282 / CC1/2: 0.97 / Rrim(I) all: 0.2 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZNY

3zny


Resolution: 1.03→42.51 Å / SU ML: 0.0944 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 11.8234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.155 5860 5 %
Rwork0.1385 111308 -
obs0.1393 117168 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.11 Å2
Refinement stepCycle: LAST / Resolution: 1.03→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 23 297 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032005
X-RAY DIFFRACTIONf_angle_d1.18852723
X-RAY DIFFRACTIONf_chiral_restr0.0936319
X-RAY DIFFRACTIONf_plane_restr0.013354
X-RAY DIFFRACTIONf_dihedral_angle_d5.802289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.2581540.23432926X-RAY DIFFRACTION78.29
1.04-1.050.25441700.19673229X-RAY DIFFRACTION87.31
1.05-1.070.1791810.17713433X-RAY DIFFRACTION92.22
1.07-1.080.181930.15943663X-RAY DIFFRACTION96.93
1.08-1.090.15741930.14353669X-RAY DIFFRACTION100
1.09-1.110.15921970.13973738X-RAY DIFFRACTION99.95
1.11-1.130.16971950.13063706X-RAY DIFFRACTION99.97
1.13-1.140.14121990.12653783X-RAY DIFFRACTION100
1.14-1.160.13061940.12183684X-RAY DIFFRACTION100
1.16-1.180.14411990.12223773X-RAY DIFFRACTION99.95
1.18-1.20.15331970.12373743X-RAY DIFFRACTION100
1.2-1.220.15411940.12623686X-RAY DIFFRACTION99.97
1.22-1.240.13671960.12433736X-RAY DIFFRACTION100
1.24-1.270.12171990.12623772X-RAY DIFFRACTION100
1.27-1.30.14621970.13473747X-RAY DIFFRACTION99.95
1.3-1.330.14341960.14383713X-RAY DIFFRACTION99.92
1.33-1.360.1631970.14183746X-RAY DIFFRACTION100
1.36-1.40.13611970.12793753X-RAY DIFFRACTION100
1.4-1.440.13712000.12083794X-RAY DIFFRACTION99.95
1.44-1.490.14891980.11493760X-RAY DIFFRACTION100
1.49-1.540.1271980.1183762X-RAY DIFFRACTION99.95
1.54-1.60.13031970.12173748X-RAY DIFFRACTION100
1.6-1.670.15222000.12513785X-RAY DIFFRACTION100
1.67-1.760.15461990.12633781X-RAY DIFFRACTION100
1.76-1.870.14091990.12623793X-RAY DIFFRACTION100
1.87-2.020.13652000.12523806X-RAY DIFFRACTION100
2.02-2.220.13452020.13053825X-RAY DIFFRACTION100
2.22-2.540.13642020.13723852X-RAY DIFFRACTION100
2.54-3.20.17562050.14823884X-RAY DIFFRACTION99.98
3.2-42.510.18942120.16624018X-RAY DIFFRACTION98.88

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