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- PDB-1f91: BETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I IN COMPLEX WITH C... -

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Basic information

Entry
Database: PDB / ID: 1f91
TitleBETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I IN COMPLEX WITH C10 FATTY ACID SUBSTRATE
ComponentsBETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / Thiolase fold family / Dimer
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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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
DECANOIC ACID / HYDROXIDE ION / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsOlsen, J.G. / Kadziola, A. / Wettstein-Knowles, P.V. / Siggaard-Andersen, M. / Larsen, S.
CitationJournal: 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.
History
DepositionJul 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 1.3Nov 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 1.4Nov 20, 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)171,43012
Polymers170,6734
Non-polymers7578
Water7,566420
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)85,7156
Polymers85,3362
Non-polymers3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-31 kcal/mol
Surface area25080 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)85,7156
Polymers85,3362
Non-polymers3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-30 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.5, 141.5, 213.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42668.191 Da / Num. of mol.: 4 / Mutation: C163S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#3: Chemical
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.4
Details: 1.9 M ammonium sulfate, 2% PEG400, 0.1 M bis-Tris propane pH 6.5, pH 7.4, VAPOR DIFFUSION, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
32 %PEG4001reservoir
40.1 Mbis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5184
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5184 Å / Relative weight: 1
ReflectionResolution: 2.4→500 Å / Num. all: 71413 / Num. obs: 70763 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.7 Å2
Reflection
*PLUS
Rmerge(I) obs: 0.052

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3565 5 %Random
Rwork0.1736 ---
all-71413 --
obs-70763 99.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.458 Å20 Å20 Å2
2---1.329 Å20 Å2
3---0.871 Å2
Refinement stepCycle: LAST / Resolution: 2.4→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11932 0 48 420 12400
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.21 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3

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