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- PDB-9ka2: Crystal structure of beta-ketoacyl-ACP synthase FabH from E. coli -

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Basic information

Entry
Database: PDB / ID: 9ka2
TitleCrystal structure of beta-ketoacyl-ACP synthase FabH from E. coli
ComponentsBeta-ketoacyl-[acyl-carrier-protein] synthase III
KeywordsBIOSYNTHETIC PROTEIN / beta-ketoacyl-ACP synthase FabH
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 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-like
Similarity search - Domain/homology
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhang, L. / Zhang, L. / Cai, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22477077 China
CitationJournal: Acs Catalysis / Year: 2025
Title: The Molecular Basis of the beta-Ketoacyl-ACP Synthase FabH in Catalyzing C-C Bond Formation of Acetoacetyl-ACP
Authors: Cai, C. / Huang, Y. / Zhang, L. / Zhang, L.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-ketoacyl-[acyl-carrier-protein] synthase III
B: Beta-ketoacyl-[acyl-carrier-protein] synthase III


Theoretical massNumber of molelcules
Total (without water)71,4372
Polymers71,4372
Non-polymers00
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-27 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.267, 64.539, 164.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-ketoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl- ...Beta-ketoacyl-ACP synthase III / KAS III / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / EcFabH


Mass: 35718.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fabH, b1091, JW1077 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris Bicine, PH8.5, 10% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.5→82.48 Å / Num. obs: 110558 / % possible obs: 99.7 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Χ2: 0.85 / Net I/σ(I): 20.3 / Num. measured all: 1354781
Reflection shellResolution: 1.5→1.58 Å / % possible obs: 98.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.644 / Num. measured all: 147409 / Num. unique obs: 15635 / CC1/2: 0.912 / Rpim(I) all: 0.218 / Rrim(I) all: 0.681 / Χ2: 0.58 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.57 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 5530 5.01 %
Rwork0.1853 --
obs0.1859 110412 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 0 602 5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074795
X-RAY DIFFRACTIONf_angle_d1.0666530
X-RAY DIFFRACTIONf_dihedral_angle_d14.4221704
X-RAY DIFFRACTIONf_chiral_restr0.087783
X-RAY DIFFRACTIONf_plane_restr0.016847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33891340.2883294X-RAY DIFFRACTION95
1.52-1.530.31342060.2723337X-RAY DIFFRACTION97
1.53-1.550.28371790.25293435X-RAY DIFFRACTION100
1.55-1.570.27992120.243447X-RAY DIFFRACTION99
1.57-1.590.24391870.23043416X-RAY DIFFRACTION100
1.59-1.610.24471850.22033494X-RAY DIFFRACTION100
1.61-1.640.22862030.21323444X-RAY DIFFRACTION100
1.64-1.660.24611670.21743474X-RAY DIFFRACTION100
1.66-1.690.26512140.21113472X-RAY DIFFRACTION100
1.69-1.720.24681820.21923463X-RAY DIFFRACTION100
1.72-1.740.22651990.21073469X-RAY DIFFRACTION100
1.74-1.780.2371570.19693493X-RAY DIFFRACTION100
1.78-1.810.20031430.19643499X-RAY DIFFRACTION100
1.81-1.850.21531950.19623504X-RAY DIFFRACTION100
1.85-1.890.21971680.19193503X-RAY DIFFRACTION100
1.89-1.930.21671900.19723445X-RAY DIFFRACTION100
1.93-1.980.2021790.1853511X-RAY DIFFRACTION100
1.98-2.030.19041780.18793520X-RAY DIFFRACTION100
2.03-2.090.20381820.18943480X-RAY DIFFRACTION100
2.09-2.160.20611670.18183515X-RAY DIFFRACTION100
2.16-2.240.19261590.18173535X-RAY DIFFRACTION100
2.24-2.330.19392030.1843506X-RAY DIFFRACTION100
2.33-2.430.21221860.18563495X-RAY DIFFRACTION100
2.43-2.560.23031760.18453529X-RAY DIFFRACTION100
2.56-2.720.20191850.18613541X-RAY DIFFRACTION100
2.72-2.930.19791880.18813561X-RAY DIFFRACTION100
2.93-3.230.18842130.18843549X-RAY DIFFRACTION100
3.23-3.690.17561860.17383569X-RAY DIFFRACTION100
3.69-4.650.14662000.15423618X-RAY DIFFRACTION100
4.65-30.570.19792070.17693764X-RAY DIFFRACTION100

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