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- PDB-9s5h: anammox-specific heterodimeric ketoacyl-ACP synthase (amxFabFhet)... -

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Basic information

Entry
Database: PDB / ID: 9s5h
Titleanammox-specific heterodimeric ketoacyl-ACP synthase (amxFabFhet) from Brocadia fulgida
Components(3-oxoacyl-(Acyl-carrier-protein) ...) x 2
KeywordsBIOSYNTHETIC PROTEIN / fatty acid biosynthesis / FabF / ketoacylsynthetase / ladderane / anaerobic ammonium oxidation / anammox
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
PHOSPHATE ION / 3-oxoacyl-(Acyl-carrier-protein) synthase / 3-oxoacyl-(Acyl-carrier-protein) synthase
Similarity search - Component
Biological speciesCandidatus Brocadia fulgida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGranatino, P. / Barends, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC Consolidator Grant 724362 (STePLADDER)European Union
CitationJournal: To Be Published
Title: beta-Ketoacyl Synthase II Homologs from a Ladderane-Producing Organism Form a Ketosynthase/Chain Length Factor-like functional heterodimer
Authors: Granatino, P. / Barends, T.
History
DepositionJul 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-oxoacyl-(Acyl-carrier-protein) synthase
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase
E: 3-oxoacyl-(Acyl-carrier-protein) synthase
F: 3-oxoacyl-(Acyl-carrier-protein) synthase
G: 3-oxoacyl-(Acyl-carrier-protein) synthase
H: 3-oxoacyl-(Acyl-carrier-protein) synthase
I: 3-oxoacyl-(Acyl-carrier-protein) synthase
J: 3-oxoacyl-(Acyl-carrier-protein) synthase
K: 3-oxoacyl-(Acyl-carrier-protein) synthase
L: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)534,31234
Polymers531,79112
Non-polymers2,52122
Water6,269348
1
B: 3-oxoacyl-(Acyl-carrier-protein) synthase
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2286
Polymers88,6322
Non-polymers5964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-46 kcal/mol
Surface area25670 Å2
2
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0936
Polymers88,6322
Non-polymers4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-69 kcal/mol
Surface area26550 Å2
3
E: 3-oxoacyl-(Acyl-carrier-protein) synthase
F: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0826
Polymers88,6322
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-51 kcal/mol
Surface area26350 Å2
4
G: 3-oxoacyl-(Acyl-carrier-protein) synthase
H: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2487
Polymers88,6322
Non-polymers6165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-62 kcal/mol
Surface area26210 Å2
5
I: 3-oxoacyl-(Acyl-carrier-protein) synthase
J: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9115
Polymers88,6322
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-37 kcal/mol
Surface area26100 Å2
6
K: 3-oxoacyl-(Acyl-carrier-protein) synthase
L: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7514
Polymers88,6322
Non-polymers1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-45 kcal/mol
Surface area26130 Å2
Unit cell
Length a, b, c (Å)113.920, 119.960, 374.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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3-oxoacyl-(Acyl-carrier-protein) ... , 2 types, 12 molecules BAEGIKCDFHJL

#1: Protein
3-oxoacyl-(Acyl-carrier-protein) synthase


Mass: 44053.379 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Brocadia fulgida (bacteria) / Gene: BROFUL_02171 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M2USV6
#2: Protein
3-oxoacyl-(Acyl-carrier-protein) synthase


Mass: 44578.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Brocadia fulgida (bacteria) / Gene: BROFUL_02170 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M2UTJ1

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Non-polymers , 8 types, 370 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) MPD, 0.1 M MES (2-(N-morpholino)ethanesulfonic acid) pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.86 Å / Num. obs: 299885 / % possible obs: 98.35 % / Redundancy: 4.9 % / Biso Wilson estimate: 51.58 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.1201 / Num. unique obs: 22978

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.86 Å / SU ML: 0.4314 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 30.0108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 14978 4.99 %
Rwork0.2189 284907 -
obs0.2212 299885 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37009 0 143 348 37500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001937795
X-RAY DIFFRACTIONf_angle_d0.481251151
X-RAY DIFFRACTIONf_chiral_restr0.04485839
X-RAY DIFFRACTIONf_plane_restr0.00376624
X-RAY DIFFRACTIONf_dihedral_angle_d13.565913834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.4224990.36539466X-RAY DIFFRACTION98.35
2.63-2.660.39355090.35229577X-RAY DIFFRACTION98.76
2.66-2.690.3874930.33389482X-RAY DIFFRACTION99
2.69-2.730.35935070.31319612X-RAY DIFFRACTION98.5
2.73-2.760.36594940.31729509X-RAY DIFFRACTION99.13
2.76-2.80.34435000.31059577X-RAY DIFFRACTION98.66
2.8-2.840.3264970.30769511X-RAY DIFFRACTION98.84
2.84-2.880.36435000.30559486X-RAY DIFFRACTION98.93
2.88-2.930.33065090.2919624X-RAY DIFFRACTION98.64
2.93-2.980.34864930.28739489X-RAY DIFFRACTION98.75
2.98-3.030.36894980.28769527X-RAY DIFFRACTION98.84
3.03-3.080.34145030.28639617X-RAY DIFFRACTION98.69
3.08-3.140.31234980.27459458X-RAY DIFFRACTION98.54
3.14-3.210.30465000.27029524X-RAY DIFFRACTION98.82
3.21-3.280.29415050.25859566X-RAY DIFFRACTION98.88
3.28-3.350.30065060.23819569X-RAY DIFFRACTION98.83
3.35-3.440.26135050.2359521X-RAY DIFFRACTION98.75
3.44-3.530.31145040.22699456X-RAY DIFFRACTION97.69
3.53-3.630.26964840.22529268X-RAY DIFFRACTION96.31
3.63-3.750.28135010.21289341X-RAY DIFFRACTION96.75
3.75-3.880.24134880.19529450X-RAY DIFFRACTION97.97
3.88-4.040.23985010.18749525X-RAY DIFFRACTION98.52
4.04-4.220.23745090.1859523X-RAY DIFFRACTION98.62
4.22-4.440.22885030.17269532X-RAY DIFFRACTION98.66
4.44-4.720.20814980.16259528X-RAY DIFFRACTION98.83
4.72-5.090.21114990.16929492X-RAY DIFFRACTION98.59
5.09-5.60.22445030.18859523X-RAY DIFFRACTION98.36
5.6-6.410.27034860.20719447X-RAY DIFFRACTION97.7
6.41-8.070.2154840.17329300X-RAY DIFFRACTION96.21
8.07-48.860.1885020.16359407X-RAY DIFFRACTION97.61

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