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- PDB-6n6v: OXA-23 mutant F110A/M221A low pH form meropenem complex -

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Basic information

Entry
Database: PDB / ID: 6n6v
TitleOXA-23 mutant F110A/M221A low pH form meropenem complex
ComponentsBeta-lactamase
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7682
Polymers27,3831
Non-polymers3851
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.114, 44.012, 46.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 27382.590 Da / Num. of mol.: 1 / Fragment: UNP residues 32-273 / 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, SAMEA104305229_06308, SAMEA104305235_03908, SAMEA104305242_04084, SAMEA104305268_03570, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305320_04271, SAMEA104305325_04185, 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 0.06 M citric acid, 0.04 M bis-Tris propane, pH 4.1, 16% 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: 1.55→38.5 Å / Num. obs: 41640 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 17.4
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1964 / Rpim(I) all: 0.414 / Rrim(I) all: 1.078

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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 4JF5

4jf5


Resolution: 1.55→36.957 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.26
RfactorNum. reflection% reflection
Rfree0.1917 2093 5.09 %
Rwork0.1722 --
obs0.1732 41131 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.39 Å2 / Biso mean: 26.2372 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 1.55→36.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 26 168 2009
Biso mean--35.61 37.29 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58610.31551350.28442525266099
1.5861-1.62570.27731050.239926102715100
1.6257-1.66970.23741300.222925462676100
1.6697-1.71880.23091610.200425572718100
1.7188-1.77430.1931520.184225722724100
1.7743-1.83770.20661540.175525442698100
1.8377-1.91130.16961510.176325442695100
1.9113-1.99830.17421240.169926122736100
1.9983-2.10360.18731370.159525922729100
2.1036-2.23540.18251420.158425702712100
2.2354-2.4080.181350.169626012736100
2.408-2.65020.19061350.177826332768100
2.6502-3.03360.20471520.175526362788100
3.0336-3.82140.20461300.164626842814100
3.8214-36.96780.16751500.159728122962100
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)
11.9052-0.3795-0.7210.82350.05572.05070.10550.30380.1399-0.2041-0.0712-0.0505-0.04770.05780.00040.14330.0107-0.01180.1679-0.01360.121620.251218.5799-7.7838
20.8043-0.4451-0.7061.5611-0.16851.9574-0.0865-0.2298-0.11040.22610.0688-0.14670.35950.2302-0.00050.25170.0357-0.020.21370.0010.144212.636411.452415.2507
32.2731-0.2024-0.18981.04020.24492.59480.0125-0.0471-0.04940.11220.00290.03640.1926-0.04310.00310.1148-0.0135-0.01830.108200.086411.75916.18773.6849
41.9568-0.38030.15430.8197-0.13211.40150.04380.07460.1840.0335-0.0614-0.2172-0.05130.0918-0.00060.1069-0.00660.00140.1167-0.01980.15224.834821.4776-1.9537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 91 )A32 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 150 )A92 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 208 )A151 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 273 )A209 - 273

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