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- PDB-5yo9: Crystal structure of KAS III from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5yo9
TitleCrystal structure of KAS III from Acinetobacter baumannii
Components3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein
KeywordsTRANSFERASE / thiolase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III family protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
Model detailsC155A mutant in complex with CoA
AuthorsLee, W.C. / Jung, M. / Lee, J. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaMSIP-2016R1A2B2008543 Korea, Republic Of
CitationJournal: to be published
Title: Crystal structure of a novel KAS III from Acinetobacter baumannii
Authors: Lee, W.C. / Jung, M. / Lee, J. / Kim, Y.
History
DepositionOct 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: 3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein
B: 3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6186
Polymers81,5742
Non-polymers1,0444
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-28 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.135, 106.942, 109.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein / KAS III / 3-oxoacyl-(Acyl carrier protein) synthase / 3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl- ...KAS III / 3-oxoacyl-(Acyl carrier protein) synthase / 3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase / KASIII / Beta-ketoacyl-ACP synthase III


Mass: 40786.852 Da / Num. of mol.: 2 / Mutation: C155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: KAS III / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: V5VGF8, beta-ketoacyl-[acyl-carrier-protein] synthase III, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.73 Å3/Da / Density % sol: 54.97 % / Mosaicity: 0.633 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2M calcium acetate, , 0.1M Tris pH 7.0, 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 58779 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 28.97 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.045 / Rrim(I) all: 0.092 / Χ2: 2.099 / Net I/σ(I): 12.3 / Num. measured all: 232845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0740.61158490.5230.3510.7091.95997.9
2.07-2.1540.47258150.6950.270.5471.94698
2.15-2.2540.39858800.8210.2290.4621.97898.5
2.25-2.3740.31958670.9040.1830.371.9798.2
2.37-2.5240.22459000.9490.1280.261.96198.4
2.52-2.7140.15458950.9740.0870.1781.97898.5
2.71-2.9940.10158980.9890.0570.1172.10297.9
2.99-3.4240.06159230.9950.0340.072.24797.6
3.42-4.3140.04158550.9980.0220.0462.495.9
4.31-503.80.03658970.9970.020.0422.45892.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LED

3led


Resolution: 2.002→27.49 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.2592 2873 4.9 %
Rwork0.2115 --
obs0.2138 58643 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.02 Å2 / Biso mean: 38.4372 Å2 / Biso min: 15.95 Å2
Refinement stepCycle: final / Resolution: 2.002→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5698 0 66 332 6096
Biso mean--40.05 36.18 -
Num. residues----737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075849
X-RAY DIFFRACTIONf_angle_d0.8797908
X-RAY DIFFRACTIONf_chiral_restr0.059897
X-RAY DIFFRACTIONf_plane_restr0.0051033
X-RAY DIFFRACTIONf_dihedral_angle_d8.0083500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.002-2.03480.35011260.33332600272696
2.0348-2.06980.34811410.32752623276498
2.0698-2.10750.36741300.31792668279898
2.1075-2.1480.34931290.30182667279698
2.148-2.19180.32181310.28092650278199
2.1918-2.23950.31091290.26952640276998
2.2395-2.29150.34781480.26832664281298
2.2915-2.34880.32031370.26312628276598
2.3488-2.41230.29361310.25582686281799
2.4123-2.48320.30491710.25222617278898
2.4832-2.56330.32471440.26012675281998
2.5633-2.65480.37421450.25352642278798
2.6548-2.76110.29711370.25062665280298
2.7611-2.88660.32211610.24392649281098
2.8866-3.03860.33091340.22692659279397
3.0386-3.22870.25321270.21482699282698
3.2287-3.47750.24821380.19482670280897
3.4775-3.82670.21171350.1752673280897
3.8267-4.37850.1831270.15652630275794
4.3785-5.50910.1791350.14562661279695
5.5091-27.49230.19431170.17082704282192

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