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- PDB-4z19: Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Y... -

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Basic information

Entry
Database: PDB / ID: 4z19
TitleCrystal structure of beta-ketoacyl-ACP synthase III (FabH) from Yersinia pestis with acetylated active site cysteine
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / FABH / FATTY ACID BIOSYNTHESIS / CONDENSING ENZYME / THIOLASE FOLD / ACETYLATED
Function / homology
Function and homology information


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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: Sci Rep / Year: 2015
Title: Structural Characterisation of the Beta-Ketoacyl-Acyl Carrier Protein Synthases, FabF and FabH, of Yersinia pestis.
Authors: Nanson, J.D. / Himiari, Z. / Swarbrick, C.M. / Forwood, J.K.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0283
Polymers33,8431
Non-polymers1842
Water4,143230
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0556
Polymers67,6872
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4700 Å2
ΔGint-30 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.460, 119.880, 49.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 33843.379 Da / Num. of mol.: 1 / Mutation: A229V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: fabH, YPO1597, y1756, YP_2257 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS
References: UniProt: Q8ZFT7, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Propan-2-ol, 0.1 M HEPES sodium salt, 15% Glycerol, 24% PEG4000, 2.25mM Acetyl-CoA, 2.25mM Malonyl-CoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→49.26 Å / Num. obs: 25320 / % possible obs: 99.3 % / Redundancy: 7.2 % / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1834)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.057 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1786 1221 4.82 %
Rwork0.1477 --
obs0.1492 25309 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 12 230 2556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062360
X-RAY DIFFRACTIONf_angle_d0.9943196
X-RAY DIFFRACTIONf_dihedral_angle_d11.645841
X-RAY DIFFRACTIONf_chiral_restr0.038375
X-RAY DIFFRACTIONf_plane_restr0.004412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.18921230.17712596X-RAY DIFFRACTION98
1.8721-1.95730.18331620.15542587X-RAY DIFFRACTION99
1.9573-2.06050.17581390.13842632X-RAY DIFFRACTION99
2.0605-2.18960.17431400.13852636X-RAY DIFFRACTION99
2.1896-2.35860.18351300.14092682X-RAY DIFFRACTION99
2.3586-2.59590.17521340.14282692X-RAY DIFFRACTION100
2.5959-2.97140.17561210.152688X-RAY DIFFRACTION100
2.9714-3.74320.17671390.14222744X-RAY DIFFRACTION100
3.7432-38.06570.18011330.15422831X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.2286 Å / Origin y: -15.5349 Å / Origin z: 25.2259 Å
111213212223313233
T0.0933 Å20.0096 Å20.0049 Å2-0.0965 Å20.0025 Å2--0.0794 Å2
L0.5825 °20.1999 °20.0692 °2-0.9547 °20.1021 °2--0.2945 °2
S0.0057 Å °0.0186 Å °-0.0686 Å °-0.0131 Å °-0.0222 Å °-0.0086 Å °0.0222 Å °0.0157 Å °0.0127 Å °
Refinement TLS groupSelection details: all

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