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- PDB-9ka6: Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in com... -

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Basic information

Entry
Database: PDB / ID: 9ka6
TitleCrystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with acyl-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 / cytosol / cytoplasm
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
Chem-6VG / 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: 1.47 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
C: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3614
Polymers80,9613
Non-polymers4001
Water17,619978
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.464, 143.325, 140.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-674-

HOH

31A-743-

HOH

41A-766-

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.: 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: 9474.341 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-6VG / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate


Mass: 400.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H25N2O8PS / 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.: 978 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
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: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.47→68.41 Å / Num. obs: 154731 / % possible obs: 96.7 % / Redundancy: 11.5 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 0.86 / Net I/σ(I): 21.8 / Num. measured all: 1782424
Reflection shellResolution: 1.47→1.55 Å / % possible obs: 85.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.612 / Num. measured all: 131670 / Num. unique obs: 19915 / CC1/2: 0.866 / Rpim(I) all: 0.247 / Rrim(I) all: 0.663 / Χ2: 0.64 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→39.14 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1783 7713 4.99 %
Rwork0.1578 --
obs0.1588 154629 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 24 978 6311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065463
X-RAY DIFFRACTIONf_angle_d0.9817444
X-RAY DIFFRACTIONf_dihedral_angle_d14.1021972
X-RAY DIFFRACTIONf_chiral_restr0.085892
X-RAY DIFFRACTIONf_plane_restr0.008968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.2812310.25314860X-RAY DIFFRACTION96
1.49-1.50.26152590.24114892X-RAY DIFFRACTION98
1.5-1.510.24641620.22683266X-RAY DIFFRACTION99
1.52-1.540.23262030.21393993X-RAY DIFFRACTION98
1.54-1.560.20872670.18525036X-RAY DIFFRACTION100
1.56-1.580.17782490.17165059X-RAY DIFFRACTION100
1.58-1.60.20742750.17164985X-RAY DIFFRACTION100
1.6-1.630.19762500.16935027X-RAY DIFFRACTION100
1.63-1.650.19712700.16785033X-RAY DIFFRACTION100
1.65-1.680.20092560.16735059X-RAY DIFFRACTION100
1.68-1.710.1822630.16755013X-RAY DIFFRACTION100
1.71-1.740.19372440.17095076X-RAY DIFFRACTION100
1.74-1.770.17362620.16275034X-RAY DIFFRACTION100
1.77-1.810.17132790.16955012X-RAY DIFFRACTION100
1.81-1.850.20132780.17355024X-RAY DIFFRACTION100
1.85-1.890.17912540.16975075X-RAY DIFFRACTION100
1.89-1.940.18512760.15985057X-RAY DIFFRACTION100
1.94-1.990.18342710.15795038X-RAY DIFFRACTION100
1.99-2.050.18372840.15195023X-RAY DIFFRACTION100
2.05-2.120.17232790.15515030X-RAY DIFFRACTION100
2.12-2.190.16622770.14775093X-RAY DIFFRACTION100
2.19-2.280.18352760.15295044X-RAY DIFFRACTION100
2.28-2.390.17562560.15935088X-RAY DIFFRACTION100
2.39-2.510.17032780.15825063X-RAY DIFFRACTION100
2.51-2.650.17762300.15624656X-RAY DIFFRACTION100
2.68-2.870.19222470.15824821X-RAY DIFFRACTION99
2.87-3.160.17122800.15715109X-RAY DIFFRACTION100
3.16-3.620.17542350.14194615X-RAY DIFFRACTION90
3.62-4.560.14792510.12764487X-RAY DIFFRACTION87
4.56-39.140.17022710.15915348X-RAY DIFFRACTION100

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