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- PDB-6n6y: OXA-23 mutant F110A/M221A neutral pH form meropenem complex -

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Basic information

Entry
Database: PDB / ID: 6n6y
TitleOXA-23 mutant F110A/M221A neutral pH form meropenem complex
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
meropenem, bound form / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.501 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)27,4712
Polymers27,0851
Non-polymers3851
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.242, 175.242, 81.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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-KE1 / meropenem, bound form / (4R,5S)-3-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S

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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: 5.75 Å3/Da / Density % sol: 78.62 %
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 22, 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: 3.5→39.2 Å / Num. obs: 8247 / % possible obs: 99.9 % / Redundancy: 14.3 % / Rpim(I) all: 0.069 / Rrim(I) all: 0.262 / Net I/σ(I): 9.4
Reflection shellResolution: 3.5→3.83 Å / Num. unique obs: 1930 / Rpim(I) all: 0.549 / Rrim(I) all: 2.071

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementStarting model: PDB entry 4JF6

4jf6


Resolution: 3.501→39.185 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2998 385 5.11 %
Rwork0.2339 7147 -
obs0.2373 7532 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.15 Å2 / Biso mean: 130.9102 Å2 / Biso min: 81.7 Å2
Refinement stepCycle: final / Resolution: 3.501→39.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 26 0 1922
Biso mean--136.88 --
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5009-4.0070.48931130.4521876198974
4.007-5.04670.25181180.210825842702100
5.0467-39.18770.27131540.187126872841100
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)
10.83030.32690.46061.12171.83642.92741.1065-1.1773-0.51851.6143-0.1620.67220.05210.3692-0.00221.4699-0.04790.24531.52110.71651.9277-16.0829-59.670820.6804
21.10590.475-1.57570.7903-0.97952.21110.2843-0.5254-1.3356-0.5128-0.41510.04130.64390.57580.00061.3060.02580.00541.32970.18922.2116-13.7836-52.56089.2667
31.38550.51321.27871.2698-0.17191.53090.3964-0.07360.83790.3026-0.0995-0.6025-0.85480.2084-0.00041.2858-0.02790.05561.15420.04041.4709-11.7738-26.83954.8032
40.8121-0.2717-0.71890.5073-0.16630.8868-0.5476-0.3712-0.07382.0313-0.00690.2977-0.877-0.10790.00081.54650.22880.05871.41720.04771.2664-23.6388-27.590314.8403
52.94592.42821.23792.6016-0.24183.81920.13550.2665-0.2252-0.34430.2616-0.16620.485-0.382-0.00031.15240.062-0.01411.1525-0.15610.9744-17.4855-35.7994-2.2851
60.16740.3097-0.2680.52470.33143.68450.4339-0.512-1.5597-0.2059-0.33871.44010.1627-0.09310.00021.1731-0.02520.15161.06550.01981.6192-15.5918-44.6893.8163
70.9167-0.6992-0.30620.5050.1510.4389-0.41180.1747-0.55730.0433-0.2663-0.8677-0.29280.0309-0.00071.1187-0.0564-0.00281.3698-0.04481.3959-2.8837-35.7947.976
83.5053-2.9674-2.65525.99041.03182.4653-0.1675-1.2094-1.66420.68060.25071.842-0.96010.57350.10771.4728-0.22370.38251.42250.50840.3433-14.7352-43.106918.4336
91.4764-0.6912-1.79850.73620.07093.19480.2272-1.0779-1.09180.7240.22411.2389-0.00380.2864-0.00011.21110.1180.29021.35120.40211.9065-14.2838-48.393816.8787
101.68780.0610.80660.16790.08050.3589-0.3654-1.6030.470.7306-0.6858-0.55890.83550.8997-0.0651.63110.32050.71721.64720.90061.2466-12.7988-51.291924.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 56 )A35 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 83 )A57 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 102 )A84 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 127 )A103 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 160 )A128 - 160
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 185 )A161 - 185
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 203 )A186 - 203
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 225 )A204 - 225
9X-RAY DIFFRACTION9chain 'A' and (resid 226 through 255 )A226 - 255
10X-RAY DIFFRACTION10chain 'A' and (resid 256 through 273 )A256 - 273

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