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- PDB-1hnj: CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III + MALONYL-COA -

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Basic information

Entry
Database: PDB / ID: 1hnj
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III + MALONYL-COA
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
MALONYL-COENZYME A / PHOSPHATE ION / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 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

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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)34,4963
Polymers33,5471
Non-polymers9492
Water4,882271
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)68,9916
Polymers67,0942
Non-polymers1,8974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7130 Å2
ΔGint-57 kcal/mol
Surface area21770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.640, 72.640, 102.490
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-496-

HOH

21A-632-

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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 38.94 %
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: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 248087 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.275 / Num. unique all: 4742 / % possible all: 98.5
Reflection
*PLUS
Num. obs: 49069 / Num. measured all: 248087
Reflection shell
*PLUS
% possible obs: 98.5 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.46→20 Å / σ(F): 0 / σ(I): 0
Details: No density for the malonyl-group and CP1-CP4 of Malonyl-CoA (MLC).
RfactorNum. reflection
Rfree0.193 -
Rwork0.169 -
obs-47015
Refinement stepCycle: LAST / Resolution: 1.46→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 53 271 2671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6

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