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- PDB-4s2n: OXA-48 in complex with Avibactam at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 4s2n
TitleOXA-48 in complex with Avibactam at pH 8.5
Components(Beta-lactamase) x 2
Keywordshydrolase/antibiotic / hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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-NXL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: ACS Infect Dis / Year: 2015
Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition.
Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Non-polymer description
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 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

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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)122,7428
Polymers121,6734
Non-polymers1,0694
Water6,936385
1
A: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3714
Polymers60,8362
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3714
Polymers60,8362
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7072
Polymers30,4401
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7072
Polymers30,4401
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6642
Polymers30,3971
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6642
Polymers30,3971
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.039, 142.039, 50.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThis protein behaves as a dimer in solution

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Components

#1: Protein Beta-lactamase /


Mass: 30439.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, FP68_27275, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: 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, blaOXA-48, FP68_27275, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#3: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M TRIS pH 8.5, 20% ethanol, 2mM avibactam, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→52.66 Å / Num. all: 76871 / Num. obs: 76256 / % possible obs: 99.2 %
Reflection shellResolution: 2→2.11 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2→52.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22293 3823 5 %RANDOM
Rwork0.19167 ---
obs0.19321 72459 99.27 %-
all-73039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.586 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-0.73 Å20 Å2
2---1.47 Å20 Å2
3---4.76 Å2
Refinement stepCycle: LAST / Resolution: 2→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 68 385 8388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0198207
X-RAY DIFFRACTIONr_bond_other_d00.027701
X-RAY DIFFRACTIONr_angle_refined_deg2.4211.92711123
X-RAY DIFFRACTIONr_angle_other_deg3.757317643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5735965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.476420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.882151424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1311548
X-RAY DIFFRACTIONr_chiral_restr0.1520.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.029341
X-RAY DIFFRACTIONr_gen_planes_other0.0310.022055
X-RAY DIFFRACTIONr_mcbond_it2.7933.2113884
X-RAY DIFFRACTIONr_mcbond_other2.7933.2113883
X-RAY DIFFRACTIONr_mcangle_it3.7234.7984841
X-RAY DIFFRACTIONr_mcangle_other3.7234.7994842
X-RAY DIFFRACTIONr_scbond_it4.3023.5974323
X-RAY DIFFRACTIONr_scbond_other4.2993.5944317
X-RAY DIFFRACTIONr_scangle_other6.2375.2296262
X-RAY DIFFRACTIONr_long_range_B_refined7.07726.32710085
X-RAY DIFFRACTIONr_long_range_B_other7.08326.279898
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 282 -
Rwork0.29 5343 -
obs--99.26 %

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