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- PDB-4ls7: Crystal structure of Bacillus subtilis beta-ketoacyl-ACP synthase... -

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Basic information

Entry
Database: PDB / ID: 4ls7
TitleCrystal structure of Bacillus subtilis beta-ketoacyl-ACP synthase II (FabF) in a non-covalent complex with cerulenin
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
Keywordstransferase/transferase inhibitor / KASII / CONDENSING ENZYME / FATTY ACID ELONGATION / DRUG TARGET / transferase-transferase inhibitor complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / 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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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
Cerulenin / : / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.674 Å
AuthorsTrajtenberg, F. / Larrieux, N. / Buschiazzo, A.
CitationJournal: Febs J. / Year: 2014
Title: Structural insights into bacterial resistance to cerulenin.
Authors: Trajtenberg, F. / Altabe, S. / Larrieux, N. / Ficarra, F. / de Mendoza, D. / Buschiazzo, A. / Schujman, G.E.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,19012
Polymers91,2192
Non-polymers97110
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-53 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.266, 87.721, 144.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 45609.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: fabF, yjaY, BSU11340 / Plasmid: pQE32L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: O34340, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1X9 / Cerulenin / (2R,3S)-3-[(4E,7E)-nona-4,7-dienoyl]oxirane-2-carboxamide


Mass: 223.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO3 / Comment: antifungal, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 0.25 M KCl, vapor diffusion, hanging drop, soaking with cerulenin (10 mg/mL) for 30 min , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2009 / Details: mirrors
RadiationMonochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.674→144.73 Å / Num. all: 105207 / Num. obs: 105207 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 18.21 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.67-1.763.40.4411.70.441195.4
1.76-1.873.50.2952.60.295198.8
1.87-23.50.1854.10.185199
2-2.163.50.1067.20.106199.5
2.16-2.373.60.07110.80.071199.7
2.37-2.653.60.05114.80.051199.9
2.65-3.063.60.036200.0361100
3.06-3.743.60.02428.80.0241100
3.74-5.293.60.01834.30.018199.9
5.29-28.9463.50.01829.40.018198.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4LS5

4ls5


Resolution: 1.674→28.921 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.14 / σ(F): 0.92 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 1051 1.01 %
Rwork0.1507 --
obs0.151 103055 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9851 Å2
Refinement stepCycle: LAST / Resolution: 1.674→28.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6137 0 60 697 6894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076577
X-RAY DIFFRACTIONf_angle_d1.1178926
X-RAY DIFFRACTIONf_dihedral_angle_d12.8892408
X-RAY DIFFRACTIONf_chiral_restr0.0771008
X-RAY DIFFRACTIONf_plane_restr0.0041185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6741-1.71590.26641420.245512564X-RAY DIFFRACTION87
1.7159-1.76230.25391550.226613408X-RAY DIFFRACTION93
1.7623-1.81420.25151320.210913505X-RAY DIFFRACTION94
1.8142-1.87270.24711160.195813605X-RAY DIFFRACTION94
1.8727-1.93960.1951400.178313622X-RAY DIFFRACTION94
1.9396-2.01730.22091250.166413617X-RAY DIFFRACTION94
2.0173-2.10910.20911220.157113695X-RAY DIFFRACTION94
2.1091-2.22020.1761450.146513697X-RAY DIFFRACTION95
2.2202-2.35930.18391220.147113720X-RAY DIFFRACTION95
2.3593-2.54130.18691490.149913737X-RAY DIFFRACTION95
2.5413-2.79690.18881440.148413777X-RAY DIFFRACTION95
2.7969-3.20110.16581680.146913716X-RAY DIFFRACTION95
3.2011-4.03140.14251370.126713800X-RAY DIFFRACTION95
4.0314-28.92490.1561480.129913967X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5572-0.07960.18171.0611-0.04440.9053-0.0003-0.07610.07120.0543-0.01370.0067-0.1275-0.14010.00940.11480.0170.0070.1352-0.01150.1064-9.043-13.503724.8554
20.7017-0.07530.23950.8313-0.13051.00170.0918-0.0433-0.1314-0.0740.00380.07390.1969-0.1356-0.07720.1455-0.0158-0.04540.12790.01110.1367-13.3232-39.776213.6436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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