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

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Basic information

Entry
Database: PDB / ID: 5yoa
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-ketodecanoyl-[acyl-carrier-protein] synthase activity / 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
OCTANOYL-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: 2.33 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)81,7513
Polymers80,8572
Non-polymers8941
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-28 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.657, 121.111, 166.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

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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: 40428.465 Da / Num. of mol.: 2 / Mutation: C155A, C264A
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-CO8 / OCTANOYL-COENZYME A


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 54.99 % / Mosaicity: 0.808 °
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: 2.33→50 Å / Num. obs: 35771 / % possible obs: 93.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Χ2: 2.554 / Net I/σ(I): 12.5 / Num. measured all: 236848
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.33-2.416.40.51131880.8870.2050.5521.82383.9
2.41-2.516.30.43532030.9130.1740.471.90884.8
2.51-2.626.30.34932490.9420.1410.3781.95285.9
2.62-2.766.10.2833680.960.1150.3042.07588.1
2.76-2.9460.21635270.9710.090.2352.13992.9
2.94-3.1660.15436890.9870.0640.1672.34196.5
3.16-3.486.30.10537980.9930.0440.1142.67599
3.48-3.986.80.07638700.9960.0310.0823.08799.9
3.98-5.027.50.06238730.9970.0240.0663.337100
5.02-508.20.05740060.9980.0210.0613.2299.3

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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: 2.33→29.908 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.2212 1828 5.12 %
Rwork0.167 --
obs0.1698 35736 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.94 Å2 / Biso mean: 31.4738 Å2 / Biso min: 10.94 Å2
Refinement stepCycle: final / Resolution: 2.33→29.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 57 265 5995
Biso mean--48.51 28.59 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075816
X-RAY DIFFRACTIONf_angle_d0.9077868
X-RAY DIFFRACTIONf_chiral_restr0.057893
X-RAY DIFFRACTIONf_plane_restr0.0051030
X-RAY DIFFRACTIONf_dihedral_angle_d8.0373486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3253-2.38810.29551200.20572239235982
2.3881-2.45840.28021240.20622360248485
2.4584-2.53770.25791340.19092368250285
2.5377-2.62830.29541140.19242390250486
2.6283-2.73350.26241270.19172469259688
2.7335-2.85780.27761290.19512534266391
2.8578-3.00830.28091300.19322667279795
3.0083-3.19660.24911680.18682699286798
3.1966-3.44310.23821580.17952772293099
3.4431-3.7890.20121480.158828092957100
3.789-4.33580.19921640.137827992963100
4.3358-5.45730.18061420.134228613003100
5.4573-29.91030.16331700.155829413111100

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