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- PDB-9ka5: Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q from E... -

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Basic information

Entry
Database: PDB / ID: 9ka5
TitleCrystal structure of beta-ketoacyl-ACP synthase FabH C112Q 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: 1.42 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,7431
Polymers35,7431
Non-polymers00
Water5,729318
1
A: Beta-ketoacyl-[acyl-carrier-protein] synthase III

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


Theoretical massNumber of molelcules
Total (without water)71,4872
Polymers71,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.481, 72.481, 101.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-635-

HOH

31A-709-

HOH

41A-716-

HOH

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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: 35743.379 Da / Num. of mol.: 1 / Mutation: C112Q
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.: 318 / 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: 1.86 Å3/Da / Density % sol: 33.79 %
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 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.42→51.25 Å / Num. obs: 53096 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.011 / Rrim(I) all: 0.052 / Χ2: 0.75 / Net I/σ(I): 28.3
Reflection shellResolution: 1.42→1.49 Å / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.495 / Num. measured all: 60098 / Num. unique obs: 7436 / CC1/2: 0.935 / Rpim(I) all: 0.181 / Rrim(I) all: 0.529 / Χ2: 0.41 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→30.87 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 2356 4.97 %
Rwork0.1736 --
obs0.1745 47368 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 0 318 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082420
X-RAY DIFFRACTIONf_angle_d1.0993302
X-RAY DIFFRACTIONf_dihedral_angle_d14.542867
X-RAY DIFFRACTIONf_chiral_restr0.085397
X-RAY DIFFRACTIONf_plane_restr0.014429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.2363850.21651627X-RAY DIFFRACTION57
1.45-1.480.2601830.19811821X-RAY DIFFRACTION64
1.48-1.510.2661930.21622108X-RAY DIFFRACTION73
1.51-1.550.23391080.20672324X-RAY DIFFRACTION82
1.55-1.590.23571360.20082534X-RAY DIFFRACTION90
1.59-1.640.20051290.20042741X-RAY DIFFRACTION96
1.64-1.690.23651590.22820X-RAY DIFFRACTION99
1.69-1.760.23241740.19672811X-RAY DIFFRACTION100
1.76-1.830.24151440.19442861X-RAY DIFFRACTION100
1.83-1.910.22761500.18562871X-RAY DIFFRACTION100
1.91-2.010.21341470.1822877X-RAY DIFFRACTION100
2.01-2.140.18031630.17632847X-RAY DIFFRACTION100
2.14-2.30.18461720.16732861X-RAY DIFFRACTION100
2.3-2.530.19491500.17672893X-RAY DIFFRACTION100
2.53-2.90.20351500.17652941X-RAY DIFFRACTION100
2.9-3.650.16711570.16162947X-RAY DIFFRACTION100
3.65-30.870.1561560.15083128X-RAY DIFFRACTION100

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