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- PDB-6n6x: OXA-23 mutant F110A/M221A neutral pH form imipenem complex -

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Basic information

Entry
Database: PDB / ID: 6n6x
TitleOXA-23 mutant F110A/M221A neutral pH form imipenem complex
ComponentsBeta-lactamase oxa23
KeywordsHYDROLASE / carbapenemase / antibiotic resistance / mutant
Function / homology
Function and homology information


penicillin binding / cell wall organization / hydrolase 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
Imipenem / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2019
Title: Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D beta-Lactamases.
Authors: Stewart, N.K. / Smith, C.A. / Antunes, N.T. / Toth, M. / Vakulenko, S.B.
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 11, 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 1.4Nov 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 oxa23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4833
Polymers27,0851
Non-polymers3972
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.851, 174.851, 81.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

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Components

#1: Protein Beta-lactamase oxa23 / Carbapenem-hydrolyzing class D beta-lactamase OXA-23 / Carbapenemase OXA-23 / Class D beta- ...Carbapenem-hydrolyzing class D beta-lactamase OXA-23 / Carbapenemase OXA-23 / Class D beta-lactamase / OXA-23 / OXA-23 carbapenemase / OXA-23 class D beta-lactamase / OXA23 carbapenemase / class D Beta-lactamase Oxa-23


Mass: 27085.176 Da / Num. of mol.: 1 / Fragment: UNP residues 35-273 / Mutation: F110A/M221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, ...Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, AZE33_05250, C7G90_19950, CAS83_19595, CBE85_20255, CBI29_04474, CEJ63_03230, DV997_16620, DVA79_19285, IX87_16825, IX87_21860, LV38_03424, NG19_0098, SAMEA104305208_04008, SAMEA104305242_04084, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305341_03854, SAMEA104305343_03919, SAMEA104305351_03822, SAMEA104305385_00775
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4P2, beta-lactamase
#2: Chemical ChemComp-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 5.74 Å3/Da / Density % sol: 78.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M succinic acid, pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→39.1 Å / Num. obs: 11718 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.189 / Net I/σ(I): 10.8
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 2056 / Rpim(I) all: 0.291 / Rrim(I) all: 1.152

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JF6

4jf6


Resolution: 3.1→39.098 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2162 570 4.87 %
Rwork0.1902 --
obs0.1915 11708 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.73 Å2 / Biso mean: 95.3963 Å2 / Biso min: 56.67 Å2
Refinement stepCycle: final / Resolution: 3.1→39.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 25 0 1927
Biso mean--114.99 --
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1003-3.41210.34171370.278727242861
3.4121-3.90550.27461370.223127322869
3.9055-4.9190.1731530.159127692922
4.919-39.1010.19361430.17629133056
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)
10.38640.3980.54451.14460.88720.91860.3116-0.2617-0.92231.60050.3183-0.07591.33290.38560.07341.2644-0.01840.72161.3347-0.29511.7153-62.022515.642723.4558
20.98480.88860.33620.8648-0.18461.3896-0.1370.03860.54780.37940.13561.03130.3436-0.3167-0.00070.9064-0.03450.20470.7904-0.15851.1254-49.849413.7549.6595
30.4550.3668-0.07140.6951-0.69511.0040.3627-0.61570.17060.1399-0.1056-0.0795-0.20680.3512-00.8516-0.0925-0.01931.0893-0.20180.6956-24.815620.737810.2077
42.30370.4173-1.4462.7498-0.56261.9257-0.28510.17390.51460.0158-0.01850.8085-0.021-0.02970.0010.788-0.0202-0.02410.7705-0.05740.8184-37.33216.99843.2832
52.93181.50040.1351.51181.16561.60240.1194-0.2320.1810.5449-0.17780.340.19840.05280.00081.0247-0.01440.15460.8253-0.03990.8035-39.65319.251613.5767
62.10660.76030.06860.49260.71052.17240.2229-0.72970.54471.0303-0.10740.51360.1727-0.04280.00021.0877-0.15440.44860.9162-0.31031.169-49.297513.636419.7166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 46 )A35 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 91 )A47 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 113 )A92 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 185 )A114 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 225 )A186 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 273 )A226 - 273

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