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- PDB-4k0x: X-ray Crystal Structure of OXA-23 from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 4k0x
TitleX-ray Crystal Structure of OXA-23 from Acinetobacter baumannii
ComponentsBeta-lactamase
KeywordsHYDROLASE / Carbapenemase
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
BICARBONATE ION / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKlinger, N.V. / Ramey, M.E. / Leonard, D.A. / Powers, R.A.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Structures of the Class D Carbapenemases OXA-23 and OXA-146: Mechanistic Basis of Activity against Carbapenems, Extended-Spectrum Cephalosporins, and Aztreonam.
Authors: Kaitany, K.C. / Klinger, N.V. / June, C.M. / Ramey, M.E. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references

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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)27,8123
Polymers27,6901
Non-polymers1222
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.000, 46.539, 136.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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 / Fragment: UNP residues 31-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ari-1, bla(OXA-23), bla-OXA-23, blaOXA-23, OXA-23, oxa23
Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L4P2, beta-lactamase
#2: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 51.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 5% w/v PGA-LM, 30% v/v PEG 550MME,0.1M Sodium acetate, OXA-23 in 50 mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 296K
PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.61→31.69 Å / Num. all: 37261 / Num. obs: 35200 / % possible obs: 99.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.8
Reflection shellResolution: 1.61→1.67 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→31.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.463 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19188 1857 5 %RANDOM
Rwork0.16395 ---
obs0.16546 35200 99.28 %-
all-37261 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.131 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2--1.55 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.61→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 8 255 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9592790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05425.87697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.645158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 124 -
Rwork0.219 2290 -
obs--96.06 %

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