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- PDB-6zxi: Crystal Structure of the OXA-48 Carbapenem-Hydrolyzing Class D be... -

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Basic information

Entry
Database: PDB / ID: 6zxi
TitleCrystal Structure of the OXA-48 Carbapenem-Hydrolyzing Class D beta-Lactamase in Complex with the DBO inhibitor ANT3310
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / carbapenemase / ANT3310 / antibiotic resistance / carbapenem-hydrolyzing beta-lactamase / diazabicyclooctanone inhibitor
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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/transpeptidase-like
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-QS8 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDocquier, J.D. / Pozzi, C. / De Luca, F. / Benvenuti, M. / Mangani, S.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of ANT3310 , a Novel Broad-Spectrum Serine beta-Lactamase Inhibitor of the Diazabicyclooctane Class, Which Strongly Potentiates Meropenem Activity against Carbapenem-Resistant ...Title: Discovery of ANT3310 , a Novel Broad-Spectrum Serine beta-Lactamase Inhibitor of the Diazabicyclooctane Class, Which Strongly Potentiates Meropenem Activity against Carbapenem-Resistant Enterobacterales and Acinetobacter baumannii.
Authors: Davies, D.T. / Leiris, S. / Zalacain, M. / Sprynski, N. / Castandet, J. / Bousquet, J. / Lozano, C. / Llanos, A. / Alibaud, L. / Vasa, S. / Pattipati, R. / Valige, R. / Kummari, B. / ...Authors: Davies, D.T. / Leiris, S. / Zalacain, M. / Sprynski, N. / Castandet, J. / Bousquet, J. / Lozano, C. / Llanos, A. / Alibaud, L. / Vasa, S. / Pattipati, R. / Valige, R. / Kummari, B. / Pothukanuri, S. / De Piano, C. / Morrissey, I. / Holden, K. / Warn, P. / Marcoccia, F. / Benvenuti, M. / Pozzi, C. / Tassone, G. / Mangani, S. / Docquier, J.D. / Pallin, D. / Elliot, R. / Lemonnier, M. / Everett, M.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4818
Polymers60,7932
Non-polymers6886
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-6 kcal/mol
Surface area19680 Å2
Unit cell
Length a, b, c (Å)44.798, 105.106, 125.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 30396.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462
Plasmid: pET-OXA48 / Details (production host): pET-9a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): MCT236(DE3) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 434 molecules

#2: Chemical ChemComp-QS8 / [[(3~{R},6~{R})-6-fluoranyl-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate


Mass: 242.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11FN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7,5), 12% PEG 4000, 3% 1-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.85→53.85 Å / Num. obs: 51511 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7403 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.85→52.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.208 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 2739 5.3 %RANDOM
Rwork0.1717 ---
obs0.1742 48721 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.7 Å2 / Biso mean: 33.25 Å2 / Biso min: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.85→52.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 42 428 4399
Biso mean--54.33 45.35 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134126
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173697
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6425602
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5858579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20223.133233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75215707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2671523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 210 -
Rwork0.29 3516 -
all-3726 -
obs--99.87 %

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