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- PDB-6n6t: OXA-23 mutant F110A/M221A low pH form -

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Basic information

Entry
Database: PDB / ID: 6n6t
TitleOXA-23 mutant F110A/M221A low pH form
ComponentsBeta-lactamase oxa23
KeywordsHYDROLASE / carbapenemase / antibiotic resistance / mutant
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / plasma membrane
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
CITRATE ANION / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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

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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)27,7002
Polymers27,5111
Non-polymers1891
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint1 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.581, 43.991, 46.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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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: 27510.721 Da / Num. of mol.: 1 / Fragment: UNP residues 31-273 / 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 51.47 %
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: Jun 13, 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: 1.25→38.5 Å / Num. obs: 77642 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 14.7
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 3601 / Rpim(I) all: 0.348 / Rrim(I) all: 0.891

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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: 1.25→38.465 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.46
RfactorNum. reflection% reflection
Rfree0.1799 3762 4.85 %
Rwork0.1543 --
obs0.1555 77642 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.31 Å2 / Biso mean: 23.2265 Å2 / Biso min: 9.4 Å2
Refinement stepCycle: final / Resolution: 1.25→38.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 13 262 2121
Biso mean--24.15 37.05 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26580.30071180.24212645276397
1.2658-1.28250.21571460.2252642278897
1.2825-1.30010.25531520.20332656280897
1.3001-1.31860.20251590.19492629278898
1.3186-1.33830.23581400.19762698283898
1.3383-1.35920.21241350.18952661279698
1.3592-1.38150.2171490.17222680282998
1.3815-1.40530.18321330.16542690282398
1.4053-1.43090.20311450.15262701284698
1.4309-1.45840.18331250.15042730285599
1.4584-1.48820.17921300.15032731286199
1.4882-1.52050.16081250.14222725285099
1.5205-1.55590.1731180.14472741285999
1.5559-1.59480.17861130.14922698281198
1.5948-1.63790.16021520.13532739289199
1.6379-1.68610.17321680.13662724289299
1.6861-1.74060.16071510.13912706285799
1.7406-1.80280.17011580.13772715287399
1.8028-1.8750.15721590.148827532912100
1.875-1.96030.18251360.14662729286599
1.9603-2.06360.15671430.141627962939100
2.0636-2.19290.1593980.141528232921100
2.1929-2.36220.16941220.149528002922100
2.3622-2.59990.19121570.158128022959100
2.5999-2.9760.19971350.16742800293599
2.976-3.74890.18541470.155628713018100
3.7489-38.48330.16781480.15152995314399

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