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- PDB-8vda: Crystal structure of Bacillus subtilis FabHA-coenzyme A complex -

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Basic information

Entry
Database: PDB / ID: 8vda
TitleCrystal structure of Bacillus subtilis FabHA-coenzyme A complex
ComponentsBeta-ketoacyl-[acyl-carrier-protein] synthase III 1
KeywordsTRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme
Function / homology
Function and homology information


branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / 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 / Thiolase-like
Similarity search - Domain/homology
COENZYME A / Beta-ketoacyl-[acyl-carrier-protein] synthase III 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRadka, C.D. / Rock, C.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI166116 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Crystal structures of the fatty acid biosynthesis initiation enzymes in Bacillus subtilis.
Authors: Radka, C.D. / Rock, C.O.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0642
Polymers34,2961
Non-polymers7681
Water1,53185
1
A: Beta-ketoacyl-[acyl-carrier-protein] synthase III 1
hetero molecules

A: Beta-ketoacyl-[acyl-carrier-protein] synthase III 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1274
Polymers68,5922
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3570 Å2
ΔGint-32 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.610, 60.610, 153.400
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-572-

HOH

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Components

#1: Protein Beta-ketoacyl-[acyl-carrier-protein] synthase III 1 / Beta-ketoacyl-ACP synthase III 1 / KAS III 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 3 1 / 3- ...Beta-ketoacyl-ACP synthase III 1 / KAS III 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 3 1 / 3-oxoacyl-[acyl-carrier-protein] synthase III 1 / Branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase 1 / bFabH1


Mass: 34296.141 Da / Num. of mol.: 1 / Mutation: Leu-Glu is inserted after the initial methionine
Source method: isolated from a genetically manipulated source
Details: Residues GSH are from a cleaved artificial affinity tag
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fabHA, fabH, fabH1, yjaX, BSU11330 / Production host: Escherichia coli (E. coli)
References: UniProt: O34746, beta-ketoacyl-[acyl-carrier-protein] synthase III, branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 50% PEG400, 0.2 mM NaCl, 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→76.7 Å / Num. obs: 19511 / % possible obs: 99.7 % / Redundancy: 7.63 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.035 / Net I/σ(I): 34.85
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 4.71 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 1349 / CC1/2: 0.836 / Rrim(I) all: 0.503 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→41.28 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1903 10 %
Rwork0.1874 --
obs0.1917 19027 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 48 85 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122434
X-RAY DIFFRACTIONf_angle_d0.9973294
X-RAY DIFFRACTIONf_dihedral_angle_d10.359355
X-RAY DIFFRACTIONf_chiral_restr0.055374
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.28071170.23011045X-RAY DIFFRACTION87
2.07-2.130.29411260.22241147X-RAY DIFFRACTION94
2.13-2.190.24061310.21161176X-RAY DIFFRACTION95
2.19-2.260.33991330.21021197X-RAY DIFFRACTION97
2.26-2.340.23491320.21161189X-RAY DIFFRACTION97
2.34-2.430.24961340.19681201X-RAY DIFFRACTION97
2.43-2.540.25221360.20681224X-RAY DIFFRACTION98
2.55-2.680.25551360.19951224X-RAY DIFFRACTION99
2.68-2.850.27051370.19661241X-RAY DIFFRACTION99
2.85-3.070.27821400.20891252X-RAY DIFFRACTION99
3.07-3.380.25731410.19681264X-RAY DIFFRACTION100
3.38-3.860.2181400.17981266X-RAY DIFFRACTION100
3.87-4.860.17351450.1451300X-RAY DIFFRACTION100
4.87-41.280.22121550.19291398X-RAY DIFFRACTION100

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