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- PDB-4jf5: Structure of OXA-23 at pH 4.1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4jf5
TitleStructure of OXA-23 at pH 4.1
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
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: 1.15 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: Chem.Biol. / Year: 2013
Title: Structural Basis for Carbapenemase Activity of the OXA-23 beta-Lactamase from Acinetobacter baumannii.
Authors: Smith, C.A. / Antunes, N.T. / Stewart, N.K. / Toth, M. / Kumarasiri, M. / Chang, M. / Mobashery, S. / Vakulenko, S.B.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8983
Polymers27,6471
Non-polymers2512
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.919, 49.651, 44.121
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27646.934 Da / Num. of mol.: 1
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, blaOXA-23, OXA-23, oxa-23, oxa23
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 0.06 M citric acid/0.04 M bis-tris propane, 16 % PEG3350, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.15→38.715 Å / Num. all: 95345 / Num. obs: 95345 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 17.92
Reflection shellResolution: 1.15→1.18 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.99 / % possible all: 87.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→38.7 Å / SU ML: 0.1 / σ(F): 1.19 / Phase error: 14.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 9182 5.03 %random 5%
Rwork0.14 ---
obs0.1411 95345 91.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 17 270 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052093
X-RAY DIFFRACTIONf_angle_d1.3422839
X-RAY DIFFRACTIONf_dihedral_angle_d14.037821
X-RAY DIFFRACTIONf_chiral_restr0.162315
X-RAY DIFFRACTIONf_plane_restr0.007364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.27493090.275445X-RAY DIFFRACTION85
1.1631-1.17680.22692970.22925567X-RAY DIFFRACTION91
1.1768-1.19110.2272630.21065843X-RAY DIFFRACTION92
1.1911-1.20620.20913460.20825727X-RAY DIFFRACTION91
1.2062-1.22210.21783230.20025728X-RAY DIFFRACTION92
1.2221-1.23880.223070.19525702X-RAY DIFFRACTION91
1.2388-1.25650.21752780.18825851X-RAY DIFFRACTION92
1.2565-1.27530.2212730.18895750X-RAY DIFFRACTION91
1.2753-1.29520.19833350.17835715X-RAY DIFFRACTION91
1.2952-1.31640.18893130.17455580X-RAY DIFFRACTION89
1.3164-1.33910.20112610.17045279X-RAY DIFFRACTION83
1.3391-1.36350.15712910.14255762X-RAY DIFFRACTION92
1.3635-1.38970.14433060.13125906X-RAY DIFFRACTION93
1.3897-1.41810.15652940.12855842X-RAY DIFFRACTION93
1.4181-1.44890.143270.11835826X-RAY DIFFRACTION93
1.4489-1.48260.13122870.11755911X-RAY DIFFRACTION93
1.4826-1.51970.12763320.10785853X-RAY DIFFRACTION93
1.5197-1.56080.14793250.1045794X-RAY DIFFRACTION93
1.5608-1.60670.1433050.10145816X-RAY DIFFRACTION92
1.6067-1.65860.13622750.10175423X-RAY DIFFRACTION85
1.6586-1.71780.12252880.10365865X-RAY DIFFRACTION93
1.7178-1.78660.13923250.10966031X-RAY DIFFRACTION96
1.7866-1.86790.13263250.11276012X-RAY DIFFRACTION96
1.8679-1.96640.14173330.11556002X-RAY DIFFRACTION95
1.9664-2.08960.13872830.11946023X-RAY DIFFRACTION95
2.0896-2.25090.13533560.12335706X-RAY DIFFRACTION92
2.2509-2.47740.16422820.1375561X-RAY DIFFRACTION88
2.4774-2.83580.1782730.14886169X-RAY DIFFRACTION97
2.8358-3.57240.15953300.15365981X-RAY DIFFRACTION95
3.5724-38.73720.18493400.15435763X-RAY DIFFRACTION92

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