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- PDB-4jf6: Structure of OXA-23 at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 4jf6
TitleStructure of OXA-23 at pH 7.0
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
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
: / DI(HYDROXYETHYL)ETHER / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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)27,9777
Polymers27,6901
Non-polymers2876
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.662, 173.662, 81.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

K

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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: 27689.936 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M succinic acid, 20% PEG3350, pH 7.0, 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→38.832 Å / Num. all: 24509 / Num. obs: 24509 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.17
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.44 / % possible all: 98

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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: 2.5→38.8 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 1999 4.86 %random 5%
Rwork0.2269 ---
obs0.2296 24509 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 12 122 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082037
X-RAY DIFFRACTIONf_angle_d1.162749
X-RAY DIFFRACTIONf_dihedral_angle_d15.62795
X-RAY DIFFRACTIONf_chiral_restr0.076301
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.31081260.26712800X-RAY DIFFRACTION100
2.5625-2.63180.29681510.25552817X-RAY DIFFRACTION100
2.6318-2.70920.37281430.24172777X-RAY DIFFRACTION100
2.7092-2.79660.30831630.23462767X-RAY DIFFRACTION100
2.7966-2.89660.2711620.22062790X-RAY DIFFRACTION100
2.8966-3.01250.26141190.21932821X-RAY DIFFRACTION100
3.0125-3.14950.31021310.22642813X-RAY DIFFRACTION100
3.1495-3.31550.30031530.23332784X-RAY DIFFRACTION100
3.3155-3.52310.34981300.22472795X-RAY DIFFRACTION100
3.5231-3.79490.24811690.21962773X-RAY DIFFRACTION100
3.7949-4.17640.25021310.19592831X-RAY DIFFRACTION100
4.1764-4.77980.26381300.19842808X-RAY DIFFRACTION100
4.7798-6.01840.24831490.23092791X-RAY DIFFRACTION100
6.0184-38.83670.31931420.26682805X-RAY DIFFRACTION100

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