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- PDB-1fj4: THE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I ... -

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Basic information

Entry
Database: PDB / ID: 1fj4
TitleTHE STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I IN COMPLEX WITH THIOLACTOMYCIN, IMPLICATIONS FOR DRUG DESIGN
ComponentsBETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / CONDENSING ENZYMES / FATTY ACID ELONGATION / THIOLACTOMYCIN / DRUG DESIGN
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
THIOLACTOMYCIN / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsPrice, A.C. / Choi, K. / Heath, R.J. / Li, Z. / White, S.W. / Rock, C.O.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Inhibition of beta-ketoacyl-acyl carrier protein synthases by thiolactomycin and cerulenin. Structure and mechanism.
Authors: Price, A.C. / Choi, K.H. / Heath, R.J. / Li, Z. / White, S.W. / Rock, C.O.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)171,4668
Polymers170,6254
Non-polymers8414
Water5,513306
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)85,7334
Polymers85,3122
Non-polymers4212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-35 kcal/mol
Surface area23890 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)85,7334
Polymers85,3122
Non-polymers4212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-33 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.073, 138.967, 211.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A and chain B. / The biological assembly is a dimer constructed from chain C and chain D.

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Components

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


Mass: 42656.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-TLM / THIOLACTOMYCIN / 4-HYDROXY-3,5-DIMETHYL-5-(2-METHYL-BUTA-1,3-DIENYL)-5H-THIOPHEN-2-ONE


Mass: 210.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, PEG 400, Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris-HCl11
21 mMdithiothreitol11
31 mMEDTA11
415 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54
DetectorType: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.27→19.96 Å / Num. all: 76664 / Num. obs: 76664 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.3
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.566 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 626204
Reflection shell
*PLUS
% possible obs: 92.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.35→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh, R.A. and Huber, R. (1991). Accurate Bond and Angle Parameters for X-ray Protein-Structure Refinement, Acta Cryst. A47, 392-400.
RfactorNum. reflectionSelection details
Rfree0.253 5720 RANDOM
Rwork0.197 --
all0.201 75201 -
obs0.201 75201 -
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 56 306 12182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.35
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7

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