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- PDB-1dd8: CRYSTAL STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHAS... -

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Basic information

Entry
Database: PDB / ID: 1dd8
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE I FROM ESCHERICHIA COLI
ComponentsBETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / THIOLASE FOLD
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 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsOlsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Lindquist, Y. / Larsen, S.
CitationJournal: 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
DepositionNov 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)170,7374
Polymers170,7374
Non-polymers00
Water9,152508
1
A: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
B: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I


Theoretical massNumber of molelcules
Total (without water)85,3692
Polymers85,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-39 kcal/mol
Surface area25070 Å2
MethodPISA
2
C: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I
D: BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I


Theoretical massNumber of molelcules
Total (without water)85,3692
Polymers85,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-39 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.62, 142.71, 213.46
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42684.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: bis-tris propane, ammonium sulfate, PEG400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7.5 / Details: Olsen, J.G., (1995) Protein Pept. Lett., 1, 246.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium sulfate1reservoir
23 %PEG4001reservoir
30.1 MHEPES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 76863 / Num. obs: 76863 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.24 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.3→30 Å / Redundancy: 1.44 % / Rmerge(I) obs: 0.119 / Num. unique all: 2025 / % possible all: 51
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 51 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.3→10 Å / Stereochemistry target values: Engh & Huber / Details: NCS restraints were used throughout the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3809 -RANDOM
Rwork0.188 ---
all-76863 --
obs-76863 94.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11932 0 0 508 12440
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.54

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