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- PDB-6n6w: OXA-23 mutant F110A/M221A neutral pH form -

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Basic information

Entry
Database: PDB / ID: 6n6w
TitleOXA-23 mutant F110A/M221A neutral pH form
ComponentsBeta-lactamase oxa23
KeywordsHYDROLASE / carbapenemase / antibiotic resistance / mutant
Function / homology
Function and homology information


penicillin binding / 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
Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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


Theoretical massNumber of molelcules
Total (without water)27,0281
Polymers27,0281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.174, 175.174, 79.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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: 27028.123 Da / Num. of mol.: 1 / Fragment: UNP residues 36-273 / 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

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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: 5.6 Å3/Da / Density % sol: 78.05 %
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: Jun 17, 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: 3.25→39.2 Å / Num. obs: 9985 / % possible obs: 99.8 % / Redundancy: 9.3 % / Rpim(I) all: 0.085 / Rrim(I) all: 0.307 / Net I/σ(I): 9.8
Reflection shellResolution: 3.25→3.51 Å / Num. unique obs: 1983 / Rpim(I) all: 0.165 / Rrim(I) all: 0.531

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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: 3.25→39.17 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.92
RfactorNum. reflection% reflection
Rfree0.29 484 4.86 %
Rwork0.245 --
obs0.247 9964 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 94.23 Å2
Refinement stepCycle: LAST / Resolution: 3.25→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 0 0 1899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.720.38471430.29923094X-RAY DIFFRACTION99
3.72-4.68560.27151590.23783126X-RAY DIFFRACTION100
4.6856-39.17290.27481820.23073260X-RAY DIFFRACTION100
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)
10.45570.4127-0.2860.4387-0.33961.54030.8807-1.12580.3821.3192-0.3077-0.32440.4924-0.2315-0.00041.09420.1302-0.2951.0001-0.6031.857415.753459.301819.9148
20.1962-0.29350.64580.80180.0861.95930.5502-0.30041.5053-0.0378-0.4838-1.1771-0.3357-0.7516-0.00080.87250.0227-0.17550.9055-0.23861.547713.87253.99619.0226
30.1324-0.27780.28771.0467-0.62460.20850.72280.1565-0.6235-0.5086-0.77451.55490.3045-0.1084-0.0040.8593-0.076-0.08070.91170.02180.545111.003827.79424.9366
40.8101-1.8335-0.27533.25180.71281.2836-0.0886-0.12220.65870.36920.0904-0.47680.33410.1280.00070.85820.00650.01780.93770.05670.481220.024529.90476.8925
50.93591.1334-0.10021.16640.7851.68790.12610.00731.15980.01730.1779-1.17940.011-0.1014-0.00040.81950.0072-0.09770.82230.18751.238116.400843.82011.5485
60.29080.08090.35290.20210.23890.4584-0.1188-0.6152-0.00191.1338-0.08210.98710.2377-0.9645-0.00090.9159-0.15060.00221.02050.01520.62852.448135.59837.6338
71.4368-1.14931.05751.2934-0.54381.1786-0.5745-0.36091.11440.38830.1362-0.6757-0.1164-0.362-0.00050.99710.0258-0.23331.0241-0.2771.0814.589742.81318.3228
80.2523-0.25130.64461.2850.07313.40140.0705-0.56771.84271.50250.2787-1.0236-0.15730.02370.00060.8311-0.0065-0.39030.9688-0.31931.584714.299148.282516.6684
90.1720.23-0.15140.3858-0.01790.3439-0.1223-0.37420.57341.2187-0.0855-1.4850.1045-0.631-0.00031.11150.3223-0.54691.292-0.58441.293912.878151.307824.3697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 36 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 58 THROUGH 81 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 83 THROUGH 101 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 102 THROUGH 150 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 151 THROUGH 185 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 186 THROUGH 202 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 203 THROUGH 225 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 226 THROUGH 255 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 256 THROUGH 273 )

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