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- PDB-8vd9: Crystal structure of Bacillus subtilis FabHA, beta-ketoacyl carri... -

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Basic information

Entry
Database: PDB / ID: 8vd9
TitleCrystal structure of Bacillus subtilis FabHA, beta-ketoacyl carrier protein synthase III
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
Beta-ketoacyl-[acyl-carrier-protein] synthase III 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)34,5032
Polymers34,2961
Non-polymers2071
Water2,270126
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)69,0074
Polymers68,5922
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3840 Å2
ΔGint-26 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.030, 61.030, 156.410
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-611-

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 inserted after MET-1
Source method: isolated from a genetically manipulated source
Details: The first three residues (GSH) are from the cleaved affinity tag used to purify the enzyme
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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.07 %
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-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→61.03 Å / Num. obs: 25612 / % possible obs: 98 % / Redundancy: 16.77 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Net I/σ(I): 22.99
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 12.34 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.87 / Num. unique obs: 1550 / CC1/2: 0.884 / Rrim(I) all: 0.609

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.24 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1999 7.98 %
Rwork0.2118 --
obs0.2148 25052 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 13 126 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032397
X-RAY DIFFRACTIONf_angle_d0.6533236
X-RAY DIFFRACTIONf_dihedral_angle_d10.109335
X-RAY DIFFRACTIONf_chiral_restr0.046370
X-RAY DIFFRACTIONf_plane_restr0.004417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.33611090.29211260X-RAY DIFFRACTION75
1.9-1.950.30091240.2511427X-RAY DIFFRACTION86
1.95-20.29381380.23531585X-RAY DIFFRACTION93
2-2.070.28361390.24481611X-RAY DIFFRACTION97
2.07-2.140.2861420.22851638X-RAY DIFFRACTION98
2.14-2.230.27631450.2341663X-RAY DIFFRACTION98
2.23-2.330.26731440.23731668X-RAY DIFFRACTION98
2.33-2.450.31671460.23861683X-RAY DIFFRACTION99
2.45-2.610.28731470.23411694X-RAY DIFFRACTION100
2.61-2.810.25711480.22631702X-RAY DIFFRACTION99
2.81-3.090.27591490.22361727X-RAY DIFFRACTION100
3.09-3.540.28681500.2121731X-RAY DIFFRACTION100
3.54-4.450.20341540.17451771X-RAY DIFFRACTION100
4.46-33.240.20921640.19881893X-RAY DIFFRACTION100

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