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- PDB-5vfd: Diazabicyclooctenone ETX2514 bound to Class D beta lactamase OXA-... -

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Basic information

Entry
Database: PDB / ID: 5vfd
TitleDiazabicyclooctenone ETX2514 bound to Class D beta lactamase OXA-24 from A. baumannii
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ETX2514 / beta-lactamase / PBP Gram negative / Astrazeneca / Entasis / A. baumannii / covalent inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9CM / Chem-9CP / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOlivier, N.B. / Lahiri, S.
CitationJournal: Nat Microbiol / Year: 2017
Title: ETX2514 is a broad-spectrum beta-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii.
Authors: Durand-Reville, T.F. / Guler, S. / Comita-Prevoir, J. / Chen, B. / Bifulco, N. / Huynh, H. / Lahiri, S. / Shapiro, A.B. / McLeod, S.M. / Carter, N.M. / Moussa, S.H. / Velez-Vega, C. / ...Authors: Durand-Reville, T.F. / Guler, S. / Comita-Prevoir, J. / Chen, B. / Bifulco, N. / Huynh, H. / Lahiri, S. / Shapiro, A.B. / McLeod, S.M. / Carter, N.M. / Moussa, S.H. / Velez-Vega, C. / Olivier, N.B. / McLaughlin, R. / Gao, N. / Thresher, J. / Palmer, T. / Andrews, B. / Giacobbe, R.A. / Newman, J.V. / Ehmann, D.E. / de Jonge, B. / O'Donnell, J. / Mueller, J.P. / Tommasi, R.A. / Miller, A.A.
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 4, 2023Group: 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6238
Polymers27,5871
Non-polymers1,0377
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-48 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.680, 102.680, 84.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-524-

HOH

31A-556-

HOH

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Components

#1: Protein Beta-lactamase / / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing ...Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase / Class D beta-lactamase OXA-40 / OXA24 B-lactamase / Oxa40


Mass: 27586.660 Da / Num. of mol.: 1 / Mutation: K84KCX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, A8G88_08245
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8RLA6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-9CP / (2S,5R)-1-formyl-4-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide


Mass: 279.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3O6S
#4: Chemical ChemComp-9CM / (2S,5R)-4-methyl-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]oct-3-ene-2-carboxamide


Mass: 277.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystallization was achieved using 6 mg/mL of enzyme in 3 mg/mL of compound in 01. MES buffer (pH 6.0) containing 2.4 M (NH4)2SO4 as the precipitant solution

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→102.68 Å / Num. obs: 33764 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 24.758 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rsym value: 0.081 / Net I/σ(I): 23.1
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4 / Num. unique obs: 3993 / Rpim(I) all: 0.189 / Rsym value: 0.488 / % possible all: 80.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC7

2jc7


Resolution: 1.93→51.34 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1698 5.06 %RANDOM
Rwork0.179 ---
obs0.18 33555 96.9 %-
Displacement parametersBiso mean: 29.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.7495 Å20 Å20 Å2
2--4.7495 Å20 Å2
3----9.499 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.93→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 73 227 2227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092072HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012813HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d755SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it2072HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2620SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.23 101 4.48 %
Rwork0.194 2155 -
all0.195 2256 -
obs--76.88 %
Refinement TLS params.Method: refined / Origin x: -24.8502 Å / Origin y: -7.0862 Å / Origin z: 10.9211 Å
111213212223313233
T-0.0476 Å20.0237 Å2-0.0246 Å2--0.0583 Å2-0.023 Å2---0.0358 Å2
L0.5562 °20.5479 °20.1206 °2-2.4642 °20.7567 °2--0.3824 °2
S0.0254 Å °-0.0509 Å °-0.0107 Å °0.0552 Å °0.0344 Å °-0.0865 Å °0.0054 Å °0.0047 Å °-0.0598 Å °
Refinement TLS groupSelection details: { A|* }

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