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- PDB-6ts9: Crystal structure of GES-5 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 6ts9
TitleCrystal structure of GES-5 carbapenemase
ComponentsBeta-lactamase
KeywordsHYDROLASE / carbapenemase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
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
BROMIDE ION / Beta-lactamase GES-5
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMaso, L. / Tondi, D. / Klein, R. / Montanari, M. / Bellio, C. / Celenza, G. / Brenk, R. / Cendron, L.
CitationJournal: Biomolecules / Year: 2020
Title: Targeting the Class A Carbapenemase GES-5 via Virtual Screening.
Authors: Klein, R. / Cendron, L. / Montanari, M. / Bellio, P. / Celenza, G. / Maso, L. / Tondi, D. / Brenk, R.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Oct 23, 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9839
Polymers62,4452
Non-polymers5387
Water9,764542
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4604
Polymers31,2221
Non-polymers2383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5225
Polymers31,2221
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.300, 80.360, 87.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 31222.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaGES-5, pGES-GZ_027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09HD0, beta-lactamase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M NaBr; 0.1 M Bis Tris propane pH 8.5; 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.55→55.33 Å / Num. obs: 78894 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.04645 / Net I/σ(I): 18.96
Reflection shellResolution: 1.55→1.605 Å / Rmerge(I) obs: 0.5643 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 7770 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNU

4gnu


Resolution: 1.55→55.33 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2037 --
Rwork0.1795 --
obs-78894 99.94 %
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 24.4365 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→55.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 16 542 4655

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