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- PDB-8ek9: Crystal structure of the class A carbapenemase CRH-1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 8ek9
TitleCrystal structure of the class A carbapenemase CRH-1 in complex with avibactam at 1.4 Angstrom resolution
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / class A carbapenemase / environmental lactamase / Chromobacterium / DBO inhibitor
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, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / beta-lactamase
Similarity search - Component
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPower, P. / Brunetti, F. / Ghiglione, B. / Guardabassi, L. / 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: Antimicrob.Agents Chemother. / Year: 2023
Title: Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC beta-Lactamases.
Authors: Brunetti, F. / Ghiglione, B. / Gudeta, D.D. / Gutkind, G. / Guardabassi, L. / Klinke, S. / Power, P.
History
DepositionSep 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,9532
Polymers28,6861
Non-polymers2671
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.500, 73.790, 51.530
Angle α, β, γ (deg.)90.000, 92.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase


Mass: 28685.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: B0T45_03570 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W0D7S2, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49 % / Description: rectangular prisms
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 22% (w/v) PEG 4,000 + 0.2 M lithium chloride + 0.1 M Tris-HCl pH 7.6

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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: 1.4→42.22 Å / Num. obs: 53514 / % possible obs: 99.6 % / Redundancy: 6.87 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 1 / Rrim(I) all: 0.033 / Net I/σ(I): 24.24
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.82 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 8539 / CC1/2: 0.814 / Rrim(I) all: 1.007 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQI

4eqi


Resolution: 1.4→42.22 Å / SU ML: 0.2003 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.8232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 2675 5 %
Rwork0.1945 50829 -
obs0.1957 53504 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 17 272 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032047
X-RAY DIFFRACTIONf_angle_d1.21252778
X-RAY DIFFRACTIONf_chiral_restr0.0973312
X-RAY DIFFRACTIONf_plane_restr0.0113364
X-RAY DIFFRACTIONf_dihedral_angle_d11.122288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.46951340.43752550X-RAY DIFFRACTION96.69
1.42-1.450.37721410.35982674X-RAY DIFFRACTION99.96
1.45-1.480.36021410.33072670X-RAY DIFFRACTION99.96
1.48-1.510.33551410.2992682X-RAY DIFFRACTION99.96
1.51-1.550.28071410.27882686X-RAY DIFFRACTION100
1.55-1.590.33771410.25832683X-RAY DIFFRACTION99.93
1.59-1.630.2911410.23632671X-RAY DIFFRACTION100
1.63-1.680.24791400.22592658X-RAY DIFFRACTION99.93
1.68-1.730.26741420.22552700X-RAY DIFFRACTION100
1.73-1.80.26221410.222677X-RAY DIFFRACTION99.96
1.8-1.870.26581390.21232672X-RAY DIFFRACTION99.89
1.87-1.950.25911420.20562689X-RAY DIFFRACTION99.93
1.95-2.050.21871420.20932700X-RAY DIFFRACTION99.96
2.05-2.180.23521410.19992669X-RAY DIFFRACTION100
2.18-2.350.22941410.20222694X-RAY DIFFRACTION100
2.35-2.590.24211430.19692698X-RAY DIFFRACTION99.93
2.59-2.960.20981410.19512684X-RAY DIFFRACTION99.96
2.96-3.730.21171430.17482716X-RAY DIFFRACTION99.9
3.73-42.220.16011400.16052656X-RAY DIFFRACTION96.75

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