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- PDB-8ehu: Crystal structure of the environmental CRH-1 class A carbapenemas... -

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Basic information

Entry
Database: PDB / ID: 8ehu
TitleCrystal structure of the environmental CRH-1 class A carbapenemase at 1.1 Angstrom resolution
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / class A carbapenemase / environmental lactamase / Chromobacterium
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
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
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 14, 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 30, 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


Theoretical massNumber of molelcules
Total (without water)28,6861
Polymers28,6861
Non-polymers00
Water10,251569
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)36.430, 72.900, 52.060
Angle α, β, γ (deg.)90.000, 92.270, 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 / Mutation: A147T,V170I,G172R
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.41 Å3/Da / Density % sol: 49 % / Description: rectangular prisms
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% (w/v) PEG 4000 + 0.2 M lithium chloride + 0.1 M Tris-HCl pH 8.5

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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: 1.1→42.34 Å / Num. obs: 105857 / % possible obs: 96.2 % / Redundancy: 6.85 % / Biso Wilson estimate: 10.62 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.052 / Net I/av σ(I): 22.6 / Net I/σ(I): 22.61
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 6 % / Mean I/σ(I) obs: 7.8 / Num. unique obs: 16478 / CC1/2: 0.986 / Rrim(I) all: 0.197 / % possible all: 98.6

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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: 1.1→42.34 Å / SU ML: 0.0829 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.7814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1786 5293 5 %
Rwork0.1654 100549 -
obs0.1661 105842 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.23 Å2
Refinement stepCycle: LAST / Resolution: 1.1→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 0 569 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822059
X-RAY DIFFRACTIONf_angle_d1.07732795
X-RAY DIFFRACTIONf_chiral_restr0.0958315
X-RAY DIFFRACTIONf_plane_restr0.0122368
X-RAY DIFFRACTIONf_dihedral_angle_d5.9035289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.19681610.20383062X-RAY DIFFRACTION88.52
1.11-1.130.18741710.17363247X-RAY DIFFRACTION93.9
1.13-1.140.16671730.17133291X-RAY DIFFRACTION93.27
1.14-1.150.18111720.17113257X-RAY DIFFRACTION94.62
1.15-1.170.18571700.17063241X-RAY DIFFRACTION94.04
1.17-1.180.19481760.16783327X-RAY DIFFRACTION94.37
1.18-1.20.17651720.16953274X-RAY DIFFRACTION94.88
1.2-1.220.16181720.16513273X-RAY DIFFRACTION94.49
1.22-1.240.19961750.17193309X-RAY DIFFRACTION95.35
1.24-1.260.17781740.16823324X-RAY DIFFRACTION94.98
1.26-1.280.16181750.16393310X-RAY DIFFRACTION95.66
1.28-1.30.17141750.16823324X-RAY DIFFRACTION95.29
1.3-1.330.17671750.16653334X-RAY DIFFRACTION96.16
1.33-1.360.19021770.16923356X-RAY DIFFRACTION96.01
1.36-1.390.1841740.16843308X-RAY DIFFRACTION96.16
1.39-1.420.18971770.16273364X-RAY DIFFRACTION96.41
1.42-1.450.17121780.16123390X-RAY DIFFRACTION96.54
1.45-1.490.17391770.16443358X-RAY DIFFRACTION96.88
1.49-1.540.17921780.16343372X-RAY DIFFRACTION96.94
1.54-1.590.16461790.15933403X-RAY DIFFRACTION97.18
1.59-1.640.1711770.15823361X-RAY DIFFRACTION97.33
1.64-1.710.1591790.16043408X-RAY DIFFRACTION97.71
1.71-1.790.18631800.16533424X-RAY DIFFRACTION97.93
1.79-1.880.19031800.16863422X-RAY DIFFRACTION98.2
1.88-20.17091810.16353439X-RAY DIFFRACTION98.29
2-2.150.17311830.15843469X-RAY DIFFRACTION98.57
2.15-2.370.17121800.16413431X-RAY DIFFRACTION98.77
2.37-2.710.18241840.17613485X-RAY DIFFRACTION99.22
2.71-3.420.19291830.16473487X-RAY DIFFRACTION99.24
3.42-42.340.17681850.16223499X-RAY DIFFRACTION98.11

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