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- PDB-1hnd: CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1hnd
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX
ComponentsBETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III
KeywordsTRANSFERASE / FabH
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsQiu, X. / Janson, C.A. / Smith, W.W. / Head, M. / Lonsdale, J. / Konstantinidis, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Refined structures of beta-ketoacyl-acyl carrier protein synthase III.
Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Head, M. / Lonsdale, J. / Konstantinidis, A.K.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Crystal Structure of Beta-Ketoacyl-Acyl Carrier Protein Synthase III. A Key Condensing Enzyme in Bacterial Fatty Acid Biosynthesis
Authors: Qiu, X. / Janson, C.A. / Konstantinidis, A.K. / Nwagwu, S. / Silverman, C. / Smith, W.W. / Khandekar, S.K. / Lonsdale, J. / Abdel-Meguid, S.S.
History
DepositionDec 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
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 III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3152
Polymers33,5471
Non-polymers7681
Water5,495305
1
A: BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III
hetero molecules

A: BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6294
Polymers67,0942
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4880 Å2
ΔGint-32 kcal/mol
Surface area23670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.510, 72.510, 102.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

21A-697-

HOH

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Components

#1: Protein BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / BETA-KETOACYL-ACP SYNTHASE III


Mass: 33547.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion / Details: Janson, C.A., (2000) Acta Crystallogr.D, 56, 747.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
350 mM1dropNaCl
42 mMdithiothreitol1drop
50.1 Mmagnesium chloride1reservoir
60.05 MTris-HCl1reservoir
715 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 29689 / % possible obs: 81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2 / Num. unique all: 1247 / % possible all: 35
Reflection
*PLUS
Num. measured all: 166321
Reflection shell
*PLUS
% possible obs: 35 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: FabH-AcCoA complex

Resolution: 1.6→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2500 -5%
Rwork0.213 ---
obs-29689 81 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 48 305 2700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 29689 / Num. reflection obs: 28319
Solvent computation
*PLUS
Displacement parameters
*PLUS

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