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- PDB-1g5x: The Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase I -

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Basic information

Entry
Database: PDB / ID: 1g5x
TitleThe Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase I
ComponentsBETA-KETOACYL ACYL CARRIER PROTEIN SYNTHASE I
KeywordsTRANSFERASE / enzyme / gene duplication
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 / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, Y.M. / Rao, M.S. / Heath, R.J. / Price, A.C. / Olson, A.J. / Rock, C.O. / White, S.W.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III.
Authors: Zhang, Y.M. / Rao, M.S. / Heath, R.J. / Price, A.C. / Olson, A.J. / Rock, C.O. / White, S.W.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)170,6254
Polymers170,6254
Non-polymers00
Water7,206400
1
A: BETA-KETOACYL ACYL CARRIER PROTEIN SYNTHASE I
B: BETA-KETOACYL ACYL CARRIER PROTEIN SYNTHASE I


Theoretical massNumber of molelcules
Total (without water)85,3122
Polymers85,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-40 kcal/mol
Surface area24230 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)85,3122
Polymers85,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-42 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.1, 139.6, 212.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the dimer formed by chains A and B / The biological assembly is the dimer formed by chains C and D

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Components

#1: Protein
BETA-KETOACYL ACYL CARRIER PROTEIN SYNTHASE I / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I / BETA-KETOACYL-ACP 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) / Gene: FABB / Production host: 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.: 400 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
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
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
220 %PEG4001reservoir
3100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 13, 1999 / Details: osmic confocal mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→19.9 Å / Num. all: 64781 / Num. obs: 64781 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5.7 / Num. unique all: 3015 / % possible all: 95.3
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: beta-ketoacyl acyl carrier protein synthase II

Resolution: 2.45→19.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 5874 RANDOM
Rwork0.199 --
all0.206 57865 -
obs0.206 57865 -
Refinement stepCycle: LAST / Resolution: 2.45→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 0 400 12220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.35
LS refinement shellResolution: 2.45→2.56 Å
RfactorNum. reflection
Rfree0.319 676
Rwork0.267 -
obs-6342
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.9 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / Rfactor Rwork: 0.267

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