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- PDB-4s2k: OXA-48 in complex with Avibactam at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 4s2k
TitleOXA-48 in complex with Avibactam at pH 7.5
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / inhibitor / beta-lactamase / hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
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 OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water9,674537
1
A: 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
2
B: 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
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)142.780, 142.780, 52.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsAuthors report that the protein behaves as a dimer in solution as determined by gel filtration

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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*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM tris pH 7.5, 0.1M ammonium chloride, 40% MPD, 5% PEG 8K, 100 mM NaCl, 2 mM 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: 2.1→52.42 Å / Num. all: 69789 / Num. obs: 69650 / % possible obs: 99.8 % / Biso Wilson estimate: 28.8 Å2
Reflection shellResolution: 2.1→2.21 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.1→42.25 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 3518 5.05 %RANDOM
Rwork0.175 ---
obs0.1766 69632 99.84 %-
all-69771 --
Displacement parametersBiso mean: 30.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.9372 Å20 Å20 Å2
2--4.9372 Å20 Å2
3----9.8744 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7962 0 68 537 8567
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088246HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0311161HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2911SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes240HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1167HARMONIC5
X-RAY DIFFRACTIONt_it8246HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_chiral_improper_torsion1040SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact10708SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2435 223 4.34 %
Rwork0.1894 4917 -
all0.1917 5140 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1366-0.0583-0.14411.0245-0.03210.3883-0.04520.0567-0.1285-0.012-0.0158-0.18820.00590.02370.061-0.08280.0018-0.0106-0.0465-0.06490.059250.7175-40.177315.29
20.6740.0957-0.00981.44160.47370.63520.07-0.0926-0.0630.1421-0.03570.09730.06-0.0548-0.0343-0.0547-0.02760.0219-0.0617-0.02510.002842.87-3.513136.0856
31.21210.25420.35480.76810.23770.61940.0094-0.17470.07210.05280.02320.0993-0.0158-0.0839-0.0326-0.08450.0124-0.009-0.0277-0.03540.005118.4035-38.76618.6048
41.30050.1142-0.03811.0887-0.19650.4698-0.03790.02340.0854-0.0563-0.0238-0.2162-0.02340.03450.0617-0.0616-0.01590.0483-0.0756-0.0420.0560.149423.829432.7842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A24 - 265
2X-RAY DIFFRACTION2{ B|* }B21 - 265
3X-RAY DIFFRACTION3{ C|* }C21 - 265
4X-RAY DIFFRACTION4{ D|* }D24 - 265

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