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- PDB-8vdb: Crystal structure of Bacillus subtilis FabHB, beta-ketoacyl carri... -

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Basic information

Entry
Database: PDB / ID: 8vdb
TitleCrystal structure of Bacillus subtilis FabHB, beta-ketoacyl carrier protein synthase III
ComponentsBeta-ketoacyl-[acyl-carrier-protein] synthase III 2
KeywordsTRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme
Function / homology
Function and homology information


branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / secondary metabolite biosynthetic process / 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 2
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2
B: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
C: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
D: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8197
Polymers150,5434
Non-polymers2763
Water6,882382
1
A: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
D: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4554
Polymers75,2712
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-31 kcal/mol
Surface area22140 Å2
MethodPISA
2
B: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
C: Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3633
Polymers75,2712
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-31 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.964, 92.718, 93.998
Angle α, β, γ (deg.)111.66, 110.13, 105.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-ketoacyl-[acyl-carrier-protein] synthase III 2 / Beta-ketoacyl-ACP synthase III 2 / KAS III 2 / 3-oxoacyl-[acyl-carrier-protein] synthase 3 2 / 3- ...Beta-ketoacyl-ACP synthase III 2 / KAS III 2 / 3-oxoacyl-[acyl-carrier-protein] synthase 3 2 / 3-oxoacyl-[acyl-carrier-protein] synthase III 2 / Branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase 2 / bFabH2


Mass: 37635.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fabHB, fabH2, yhfB, BSU10170 / Production host: Escherichia coli (E. coli)
References: UniProt: O07600, beta-ketoacyl-[acyl-carrier-protein] synthase III, branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 4.15 Å3/Da / Density % sol: 70.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% MPD, 0.1 M HEPES, pH 6.5

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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: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→77.14 Å / Num. obs: 88179 / % possible obs: 93.2 % / Redundancy: 3.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.182 / Net I/σ(I): 4.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4618 / CC1/2: 0.743 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.2 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1994 2.26 %
Rwork0.2057 --
obs0.2062 88082 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9916 0 18 382 10316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410091
X-RAY DIFFRACTIONf_angle_d0.78913660
X-RAY DIFFRACTIONf_dihedral_angle_d6.3511402
X-RAY DIFFRACTIONf_chiral_restr0.0471595
X-RAY DIFFRACTIONf_plane_restr0.0071729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30321210.28756246X-RAY DIFFRACTION94
2.46-2.530.31781640.27116265X-RAY DIFFRACTION95
2.53-2.60.29891000.26126316X-RAY DIFFRACTION95
2.6-2.680.2641620.24126207X-RAY DIFFRACTION94
2.68-2.780.24691450.236226X-RAY DIFFRACTION94
2.78-2.890.26911310.23116064X-RAY DIFFRACTION92
2.89-3.020.23691220.2415627X-RAY DIFFRACTION85
3.02-3.180.25911590.23826246X-RAY DIFFRACTION95
3.18-3.380.29231450.22936336X-RAY DIFFRACTION96
3.38-3.640.25291570.21986241X-RAY DIFFRACTION95
3.64-4.010.20681440.19426157X-RAY DIFFRACTION93
4.01-4.590.21231370.17195760X-RAY DIFFRACTION87
4.59-5.780.17961750.17566328X-RAY DIFFRACTION96
5.78-45.20.20171320.17776069X-RAY DIFFRACTION92

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