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- PDB-9ka7: Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in com... -

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Basic information

Entry
Database: PDB / ID: 9ka7
TitleCrystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with malonyl-ACP from E. coli
Components
  • Acyl carrier protein
  • Beta-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 / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process ...beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / membrane / cytoplasm / 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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
: / Acyl carrier protein / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: Beta-ketoacyl-[acyl-carrier-protein] synthase III
C: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6154
Polymers81,1863
Non-polymers4281
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.679, 143.305, 140.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2 / 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: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 9699.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP, b1094, JW1080 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6A8
#3: Chemical ChemComp-A1EE0 / 3-[2-[3-[[(2R)-4-bis(oxidanyl)phosphanyloxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-oxidanylidene-propanoic acid


Mass: 428.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H25N2O9PS / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0M sodium chloride,0.1M HEPES PH7.0

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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 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42002 / % possible obs: 99.4 % / Redundancy: 12.4 % / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.064 / Rrim(I) all: 0.229 / Χ2: 1.09 / Net I/σ(I): 3.1 / Num. measured all: 520041
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.389.50.6440660.840.9560.2070.6750.9597.2
2.38-2.4810.90.58840730.8990.9730.180.6170.94698.1
2.48-2.5911.80.53841610.9250.980.1610.5630.96299
2.59-2.7312.30.48941430.950.9870.1450.510.98199.9
2.73-2.913.10.42141890.9630.9910.120.4380.967100
2.9-3.1213.60.32842210.9780.9940.0920.3410.975100
3.12-3.4413.50.23442150.9850.9960.0660.2431.023100
3.44-3.93130.15442370.9910.9980.0440.161.111100
3.93-4.9513.50.1142680.9890.9970.0310.1141.18100
4.95-5012.50.11344290.9610.990.0330.1181.715100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1870 5.08 %
Rwork0.1641 --
obs0.1663 36832 87.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 0 395 5743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075432
X-RAY DIFFRACTIONf_angle_d0.9627388
X-RAY DIFFRACTIONf_dihedral_angle_d16.8471938
X-RAY DIFFRACTIONf_chiral_restr0.053879
X-RAY DIFFRACTIONf_plane_restr0.008962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.2831740.20291727X-RAY DIFFRACTION56
2.36-2.430.2599920.18431929X-RAY DIFFRACTION63
2.43-2.510.25241280.18192156X-RAY DIFFRACTION71
2.51-2.60.26631350.18132365X-RAY DIFFRACTION78
2.6-2.710.23751460.18162573X-RAY DIFFRACTION85
2.71-2.830.22711430.18382858X-RAY DIFFRACTION93
2.83-2.980.23791500.1882958X-RAY DIFFRACTION97
2.98-3.160.21731590.17952993X-RAY DIFFRACTION97
3.16-3.410.22531560.16523010X-RAY DIFFRACTION98
3.41-3.750.18321600.14743069X-RAY DIFFRACTION99
3.75-4.290.15851800.13153073X-RAY DIFFRACTION100
4.29-5.40.17731620.14093103X-RAY DIFFRACTION99
5.4-26.460.21981850.18633148X-RAY DIFFRACTION98

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