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- PDB-1b3n: BETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICAT... -

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Basic information

Entry
Database: PDB / ID: 1b3n
TitleBETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICATIONS FROM THE CRYSTAL STRUCTURE OF A COMPLEX WITH THE INHIBITOR CERULENIN.
ComponentsPROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
KeywordsCONDENSING ENZYMES / FATTY ACID ELONGATION / CERULENIN INHIBITION / LIPID METABOLISM / DRUG DESIGN / DRUG TARGET
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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
Chem-CER / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.65 Å
AuthorsMoche, M. / Schneider, G. / Edwards, P. / Dehesh, K. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure of the complex between the antibiotic cerulenin and its target, beta-ketoacyl-acyl carrier protein synthase.
Authors: Moche, M. / Schneider, G. / Edwards, P. / Dehesh, K. / Lindqvist, Y.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1842
Polymers42,9581
Non-polymers2251
Water95553
1
A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules

A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3674
Polymers85,9172
Non-polymers4512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7360 Å2
ΔGint-47 kcal/mol
Surface area26310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.394, 76.394, 147.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)


Mass: 42958.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: FABF / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[PREP4]
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE CERULENIN RESIDUE IS GIVEN CHAIN IDENTIFIER A AND RESIDUE NUMBER 413.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growpH: 8
Details: 5.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL WERE MIXED (2+2UL) WITH A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000 0.1% ...Details: 5.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL WERE MIXED (2+2UL) WITH A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000 0.1% V/V 2-MERCAPTOETHANOL AND WATER. CRYSTALS APPEARED IN A FEW DAYS
Components of the solutions
IDNameCrystal-IDSol-ID
15.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL11
2A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000, 0.1% V/V 2-MERCAPTOETHANOL AND WATER.12
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.3 M1dropNaCl
325 mMTris-HCl1drop
45 mMimidazole1drop
510 %(v/v)glycerol1drop
626 %(w/v)PEG80001reservoir
70.1 %(v/v)2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.958
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 12600 / % possible obs: 83.4 % / Redundancy: 1.8 % / Rsym value: 0.095 / Net I/σ(I): 5.3
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.325 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 22896 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 71.8 % / Rmerge(I) obs: 0.325

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Processing

Software
NameVersionClassification
SIGMAAmodel building
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
SIGMAAphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RAMACHANDRAN PLOT, PERCENT OF NON- GLYCINE OR NON-PROLINE RESIDUES IN MOST FAVOURED REGION 88.9% ADDITIONAL ALLOWED REGION 10.5% GENEROUSLY ALLOWED REGION 0.3% DISALLOWED REGION 0.3% BOND ...Details: RAMACHANDRAN PLOT, PERCENT OF NON- GLYCINE OR NON-PROLINE RESIDUES IN MOST FAVOURED REGION 88.9% ADDITIONAL ALLOWED REGION 10.5% GENEROUSLY ALLOWED REGION 0.3% DISALLOWED REGION 0.3% BOND LENGTHS (A) : 0.008 BOND ANGLES ( DEGREES) : 1.7 DIHEDRAL ANGLES (DEGREES) : 26.2 IMPROPER ANGLES (DEGREES) : 1.8
RfactorNum. reflection% reflectionSelection details
Rfree0.27 631 5 %EVERY 20TH REFLECTION
Rwork0.213 ---
obs-22896 83.4 %-
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 16 53 3074
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11926 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.08
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg26.2
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.8

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