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- PDB-6skq: OXA-655_MEM. Structural insights into the enhanced carbapenemase ... -

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Basic information

Entry
Database: PDB / ID: 6skq
TitleOXA-655_MEM. Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10.
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / Class D beta-lactamase / crystal structures / Carbapenemases / Antibiotic resistance
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MER / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeiros, H.-K.S.
CitationJournal: Febs Open Bio / Year: 2020
Title: Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10.
Authors: Leiros, H.S. / Thomassen, A.M. / Samuelsen, O. / Flach, C.F. / Kotsakis, S.D. / Larsson, D.G.J.
History
DepositionAug 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Aug 5, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,52613
Polymers118,5034
Non-polymers2,0229
Water17,475970
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2156
Polymers59,2522
Non-polymers9634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area20370 Å2
MethodPISA
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3117
Polymers59,2522
Non-polymers1,0595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-41 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.137, 82.437, 99.004
Angle α, β, γ (deg.)90.000, 97.007, 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: 29625.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaOXA-655, blaOXA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A386YIZ1, beta-lactamase
#2: Chemical
ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 6.8 mg/mL, 20-23% PEG 3350 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 61827 / % possible obs: 94.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.979 / Rrim(I) all: 0.185 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 4483 / CC1/2: 0.539 / Rrim(I) all: 0.824

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s2o

4s2o


Resolution: 2.1→24.05 Å / SU ML: 0.2467 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5815
RfactorNum. reflection% reflection
Rfree0.2348 2426 3.93 %
Rwork0.1793 --
obs0.1815 61782 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7762 0 129 970 8861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00748129
X-RAY DIFFRACTIONf_angle_d0.75110994
X-RAY DIFFRACTIONf_chiral_restr0.0461202
X-RAY DIFFRACTIONf_plane_restr0.0041386
X-RAY DIFFRACTIONf_dihedral_angle_d3.03776183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.31121350.24553411X-RAY DIFFRACTION95.79
2.14-2.190.25231420.23353513X-RAY DIFFRACTION97.83
2.19-2.240.30861490.23253433X-RAY DIFFRACTION97.63
2.24-2.30.32341330.21983536X-RAY DIFFRACTION97.68
2.3-2.360.26921590.22033484X-RAY DIFFRACTION97.77
2.36-2.430.26421400.19553490X-RAY DIFFRACTION97.61
2.43-2.510.2571310.20043207X-RAY DIFFRACTION90.22
2.51-2.60.30861450.19623546X-RAY DIFFRACTION98.64
2.6-2.70.23711480.18623546X-RAY DIFFRACTION98.96
2.7-2.820.24121560.18613546X-RAY DIFFRACTION98.96
2.82-2.970.20641350.18593560X-RAY DIFFRACTION98.85
2.97-3.160.27381490.1883518X-RAY DIFFRACTION98.95
3.16-3.40.2531430.17883543X-RAY DIFFRACTION98.27
3.4-3.740.23571260.15853306X-RAY DIFFRACTION92.33
3.74-4.280.14791520.13563629X-RAY DIFFRACTION99.63
4.28-5.380.17841490.12453581X-RAY DIFFRACTION99.1
5.38-24.050.2071340.17583507X-RAY DIFFRACTION94.79

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