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

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Basic information

Entry
Database: PDB / ID: 5yzu
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
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III family protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.122 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
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
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 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


Theoretical massNumber of molelcules
Total (without water)80,9852
Polymers80,9852
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-24 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.004, 88.395, 77.613
Angle α, β, γ (deg.)90.000, 116.480, 90.000
Int Tables number5
Space group name H-MC121

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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: 40492.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.27 Å3/Da / Density % sol: 45.93 % / Mosaicity: 2.1 °
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 315 / 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: 2.1→50 Å / Num. obs: 39643 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 37.17 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.044 / Rrim(I) all: 0.08 / Χ2: 2.812 / Net I/σ(I): 14.7 / Num. measured all: 117368
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.182.70.46740100.8130.330.5752.1799.2
2.18-2.262.70.45439410.8560.3190.5582.25198.8
2.26-2.372.70.37139740.8810.2590.4552.44798.6
2.37-2.492.80.29439580.930.2050.362.59198.4
2.49-2.652.80.22439070.9520.1550.2742.80197.8
2.65-2.852.90.16539200.970.1130.2013.11297.6
2.85-3.1430.10839560.9860.0720.1313.33698.1
3.14-3.593.20.06839830.9940.0440.0813.5999
3.59-4.523.30.04639640.9960.0290.0543.19497.7
4.52-503.40.03540300.9980.0220.0422.36298

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LED

3led


Resolution: 2.122→28.755 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.95
RfactorNum. reflection% reflection
Rfree0.2554 1999 5.06 %
Rwork0.1978 --
obs0.2007 39542 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.41 Å2 / Biso mean: 45.2872 Å2 / Biso min: 23.42 Å2
Refinement stepCycle: final / Resolution: 2.122→28.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5677 0 0 168 5845
Biso mean---40.52 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085761
X-RAY DIFFRACTIONf_angle_d0.9077787
X-RAY DIFFRACTIONf_chiral_restr0.058888
X-RAY DIFFRACTIONf_plane_restr0.0051026
X-RAY DIFFRACTIONf_dihedral_angle_d7.1163473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1219-2.1750.40141070.3152005211272
2.175-2.23380.36861410.27372726286799
2.2338-2.29950.31351480.25542729287798
2.2995-2.37360.32111530.26132726287999
2.3736-2.45840.3461260.2572764289098
2.4584-2.55680.281580.23822703286198
2.5568-2.67310.29541440.24292725286997
2.6731-2.81390.32651420.23842662280497
2.8139-2.990.29891330.22842731286497
2.99-3.22060.29361530.22712723287698
3.2206-3.54420.27531500.1952779292999
3.5442-4.05580.23171460.16672715286198
4.0558-5.10530.17771460.14772750289698
5.1053-28.75790.2071520.16842805295798

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