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- PDB-4s2j: OXA-48 in complex with Avibactam at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4s2j
TitleOXA-48 in complex with Avibactam at pH 6.5
ComponentsBeta-lactamase
KeywordsHydrolase/antibiotic / Hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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 / 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: 2.54 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 20, 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 1.4Nov 20, 2024Group: 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_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)122,6568
Polymers121,5874
Non-polymers1,0694
Water3,333185
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3284
Polymers60,7932
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3284
Polymers60,7932
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 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
4
B: 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
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)64.050, 108.100, 162.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPPROPROAA25 - 26525 - 265
21TRPTRPPROPROBB25 - 26525 - 265
12TRPTRPILEILEAA25 - 26425 - 264
22TRPTRPILEILECC25 - 26425 - 264
13TRPTRPILEILEAA25 - 26425 - 264
23TRPTRPILEILEDD25 - 26425 - 264
14TRPTRPILEILEBB25 - 26425 - 264
24TRPTRPILEILECC25 - 26425 - 264
15TRPTRPILEILEBB25 - 26425 - 264
25TRPTRPILEILEDD25 - 26425 - 264
16GLUGLUPROPROCC24 - 26524 - 265
26GLUGLUPROPRODD24 - 26524 - 265

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThis protein behaves as a dimer in solution

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Components

#1: Protein
Beta-lactamase


Mass: 30396.721 Da / Num. of mol.: 4
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: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M (NH4)2SO4, 0.1 M MES pH 6.5, 10 mM CoCl2, 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: 2.54→65.03 Å / Num. all: 37797 / Num. obs: 34471 / % possible obs: 91.2 %
Reflection shellResolution: 2.54→2.65 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→65.03 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.005 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 9.063 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22215 1700 4.9 %RANDOM
Rwork0.18377 ---
obs0.18568 32724 90.36 %-
all-35881 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.932 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.82 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.54→65.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 68 185 8147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198174
X-RAY DIFFRACTIONr_bond_other_d0.0060.027690
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.92111064
X-RAY DIFFRACTIONr_angle_other_deg1.531317609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28124.412417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.022151421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6571548
X-RAY DIFFRACTIONr_chiral_restr0.0840.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029306
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022052
X-RAY DIFFRACTIONr_mcbond_it2.4873.2023877
X-RAY DIFFRACTIONr_mcbond_other2.4873.2023877
X-RAY DIFFRACTIONr_mcangle_it3.8894.7954834
X-RAY DIFFRACTIONr_mcangle_other3.8894.7954835
X-RAY DIFFRACTIONr_scbond_it3.0933.5284297
X-RAY DIFFRACTIONr_scbond_other3.0933.5284298
X-RAY DIFFRACTIONr_scangle_other5.0165.1646231
X-RAY DIFFRACTIONr_long_range_B_refined7.02325.8699498
X-RAY DIFFRACTIONr_long_range_B_other7.01925.899464
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A153260.1
12B153260.1
21A152660.09
22C152660.09
31A152370.1
32D152370.1
41B153860.09
42C153860.09
51B152100.1
52D152100.1
61C155160.09
62D155160.09
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 112 -
Rwork0.297 2331 -
obs--88.9 %

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