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- PDB-1ek4: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH D... -

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Basic information

Entry
Database: PDB / ID: 1ek4
TitleBETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH DODECANOIC ACID TO 1.85 RESOLUTION
ComponentsBETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / fatty acid synthase / thiolase fold / Claisen condensation / fatty acid substrate complex
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsOlsen, J.G. / Kadziola, A. / Siggaard-Andersen, M. / von Wettstein-Knowles, P. / Larsen, S.
Citation
Journal: Structure / Year: 2001
Title: Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery.
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Larsen, S.
#1: Journal: FEBS Lett. / Year: 1999
Title: The X-ray crystal structure of beta-ketoacyl [acyl carrier protein] synthase I
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Lindquist, Y. / Larsen, S.
History
DepositionMar 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
B: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
C: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
D: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,0968
Polymers176,2954
Non-polymers8014
Water14,160786
1
A: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
B: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5484
Polymers88,1472
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-29 kcal/mol
Surface area25140 Å2
MethodPISA
2
C: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
D: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5484
Polymers88,1472
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-29 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.64, 142.26, 213.74
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological entity is a dimer. There are two dimers in the asymmetric unit, one defined by chains A and B and one defined by chains C and D

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Components

#1: Protein
BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I / KAS I


Mass: 44073.707 Da / Num. of mol.: 4
Mutation: C163S, MRGSHHHHHHGS N-TERMINAL HIS-TAG (NOT IN MODEL)
Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.8 M ammonium sulfate, 2 % PEG400, 0.1 M bis-Tris propane, pH 6.5, resulting pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
30.1 MBis-Tris propane1reservoir
42 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 260 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→28.92 Å / Num. obs: 131071 / % possible obs: 85 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.85→1.97 Å / Rmerge(I) obs: 0.267 / Num. unique all: 15875 / % possible all: 65.1
Reflection
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
CNS0.9refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 1.85→28.92 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Eng & Huber
RfactorNum. reflectionSelection details
Rfree0.196 6606 Random
Rwork0.173 --
obs-131071 -
Refinement stepCycle: LAST / Resolution: 1.85→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11932 0 56 782 12770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedrals_d23.1
X-RAY DIFFRACTIONc_improper_d0.76
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3

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