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- PDB-9s5i: anammox-specific heterodimeric ketoacyl-ACP synthase (amxFabFhet)... -

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Basic information

Entry
Database: PDB / ID: 9s5i
Titleanammox-specific heterodimeric ketoacyl-ACP synthase (amxFabFhet) from Brocadia fulgida in complex with its anammox-specific acyl carrier protein (amxACP)
Components
  • (3-oxoacyl-(Acyl-carrier-protein) ...) x 2
  • Acyl carrier protein
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 ...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 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-9EF / PHOSPHATE ION / 3-oxoacyl-(Acyl-carrier-protein) synthase / 3-oxoacyl-(Acyl-carrier-protein) synthase / Acyl carrier protein
Similarity search - Component
Biological speciesCandidatus Brocadia fulgida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
B: 3-oxoacyl-(Acyl-carrier-protein) synthase
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase
E: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,75913
Polymers186,2775
Non-polymers1,4828
Water9,926551
1
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3736
Polymers88,6322
Non-polymers7414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-oxoacyl-(Acyl-carrier-protein) synthase
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
E: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3867
Polymers97,6453
Non-polymers7414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.596, 163.211, 101.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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3-oxoacyl-(Acyl-carrier-protein) ... , 2 types, 4 molecules ABCD

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


Mass: 44053.379 Da / Num. of mol.: 2
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.: 2
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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Protein , 1 types, 1 molecules E

#3: Protein Acyl carrier protein


Mass: 9013.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Brocadia fulgida (bacteria) / Gene: BROFUL_02173 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M2UU63

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Non-polymers , 5 types, 559 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.07→68 Å / Num. obs: 799423 / % possible obs: 93.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 30.01 Å2 / Rpim(I) all: 0.063 / Net I/σ(I): 21.1
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 50904 / Rpim(I) all: 0.659

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→67.93 Å / SU ML: 0.2301 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 5892 5.03 %
Rwork0.187 111340 -
obs0.1887 117232 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.44 Å2
Refinement stepCycle: LAST / Resolution: 2.07→67.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12916 0 90 551 13557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003413284
X-RAY DIFFRACTIONf_angle_d0.621517977
X-RAY DIFFRACTIONf_chiral_restr0.04892058
X-RAY DIFFRACTIONf_plane_restr0.00492322
X-RAY DIFFRACTIONf_dihedral_angle_d14.20044866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.33611400.30783153X-RAY DIFFRACTION81.79
2.1-2.120.32621610.30923318X-RAY DIFFRACTION84.9
2.12-2.150.31211840.28923469X-RAY DIFFRACTION89.21
2.15-2.180.31631860.28913581X-RAY DIFFRACTION92.92
2.18-2.20.30141940.27463777X-RAY DIFFRACTION97.54
2.2-2.230.30012210.25243889X-RAY DIFFRACTION99.85
2.23-2.270.32881620.26343150X-RAY DIFFRACTION81.18
2.27-2.30.24062120.22753832X-RAY DIFFRACTION100
2.3-2.340.27042200.22353867X-RAY DIFFRACTION99.95
2.34-2.370.25741990.21553927X-RAY DIFFRACTION100
2.37-2.420.24072270.20663863X-RAY DIFFRACTION100
2.42-2.460.22972100.19583862X-RAY DIFFRACTION100
2.46-2.510.2311990.19693901X-RAY DIFFRACTION100
2.51-2.560.23172060.19393895X-RAY DIFFRACTION100
2.56-2.610.23352070.1923902X-RAY DIFFRACTION100
2.61-2.660.24251260.18682743X-RAY DIFFRACTION97.88
2.68-2.740.22212080.18773686X-RAY DIFFRACTION98.91
2.74-2.820.23321920.18853898X-RAY DIFFRACTION100
2.82-2.90.2572130.19633889X-RAY DIFFRACTION100
2.9-2.990.24352260.18723909X-RAY DIFFRACTION100
2.99-3.10.20462060.17813906X-RAY DIFFRACTION100
3.1-3.220.21812090.17273912X-RAY DIFFRACTION100
3.22-3.370.22632210.16943907X-RAY DIFFRACTION100
3.37-3.550.21681700.17633129X-RAY DIFFRACTION79.53
3.55-3.770.20871830.16333305X-RAY DIFFRACTION83.91
3.77-4.060.17931630.14833483X-RAY DIFFRACTION87.48
4.06-4.470.17412000.14343978X-RAY DIFFRACTION100
4.47-5.120.18342060.14874004X-RAY DIFFRACTION100
5.12-6.440.19452140.1834017X-RAY DIFFRACTION100
6.45-67.930.19732270.18374188X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.15368468152-0.18059721292-0.1340273734741.768893871630.1471056385131.336181545030.102291459767-0.171189446868-0.5938521864020.0811671062015-0.06931574476420.3460862587470.476075148878-0.3800765244930.005024583717440.57150160755-0.18417090059-0.06530394693580.4089613435910.06728488842890.426810857956-25.3036742032-22.2612136879-44.5684443171
21.321670155520.2775582239870.1228038579381.598275089880.1927231625370.732032874146-0.004359242154960.008004577665880.158842493923-0.108288427884-0.00195002658933-0.0471464708034-0.0759295921949-0.01299571267090.004777046543290.1368934684370.0002131743319450.02150323885220.1783684727990.004660780973940.1957975646532.7385968759233.6153983102-4.70476563142
31.36245278759-0.06927600891580.03544934762161.54375406166-0.05550553671430.704609634525-0.0221884005172-0.1056301264320.03466873907080.0665142527749-0.004538674384780.160529560759-0.0337664855122-0.08728851479920.02385760571720.128636747420.01366863822590.01717153665050.181938778364-0.02316167176360.159872400412-22.11990873718.52129227552.09363556823
42.002187771060.216577186137-0.122653677041.835961350360.3729068729012.332101534580.0305880850742-0.05006470386190.116826141851-0.190203365018-0.08724507556150.297936452218-0.237332743391-0.5146747107120.0567403929950.3732018620140.0456511186242-0.04816149872140.360170210569-0.002037336925040.226109834337-28.16533571276.77076690409-51.367093495
55.31182255616-0.008011672722490.2320574980589.137624036990.9326603139455.966540800190.0507539767702-0.1655035967520.8708500117850.14657481785-0.006348840476380.0415026451642-0.5671372579820.304063849122-0.02103842492790.736550178224-0.03503684885650.07885237777730.520018497323-0.1704327664650.704601577907-17.035737742260.523991468812.9424422317
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
11(chain 'A' and resid 4 through 408)AA4 - 4081 - 405
22( (chain 'B' and resid 4 through 408) or (chain 'A' and resid 501) )A - BC - E501 - 408405
33(chain 'C' and resid 3 through 413)CG3 - 4131 - 411
44(chain 'D' and resid 3 through 413)DJ3 - 4131 - 411
55(chain 'E' )EM4 - 831 - 80

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