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- PDB-1zow: Crystal Structure of S. aureus FabH, beta-ketoacyl carrier protei... -

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Basic information

Entry
Database: PDB / ID: 1zow
TitleCrystal Structure of S. aureus FabH, beta-ketoacyl carrier protein synthase III
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / FabH / fatty acid biosynthesis
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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsQiu, X. / Choudhry, A.E. / Janson, C.A. / Grooms, M. / Daines, R.A. / Lonsdale, J.T. / Khandekar, S.S.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure and substrate specificity of the beta-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus.
Authors: Qiu, X. / Choudhry, A.E. / Janson, C.A. / Grooms, M. / Daines, R.A. / Lonsdale, J.T. / Khandekar, S.S.
History
DepositionMay 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE According to the author residues VAL60, GLU171 and LEU287 are correct based on the electron density.

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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 III
B: 3-oxoacyl-[acyl-carrier-protein] synthase III
C: 3-oxoacyl-[acyl-carrier-protein] synthase III
D: 3-oxoacyl-[acyl-carrier-protein] synthase III


Theoretical massNumber of molelcules
Total (without water)135,6664
Polymers135,6664
Non-polymers00
Water14,268792
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase III
B: 3-oxoacyl-[acyl-carrier-protein] synthase III


Theoretical massNumber of molelcules
Total (without water)67,8332
Polymers67,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-27 kcal/mol
Surface area21500 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier-protein] synthase III
D: 3-oxoacyl-[acyl-carrier-protein] synthase III


Theoretical massNumber of molelcules
Total (without water)67,8332
Polymers67,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.900, 93.600, 110.000
Angle α, β, γ (deg.)90.00, 93.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33916.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NXE2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.2 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG3K, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 84128 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HN9

1hn9


Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 4200 5% random
Rwork0.211 --
obs0.211 84128 -
all-84128 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 0 792 10248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5

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