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- PDB-2vb8: beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibi... -

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Basic information

Entry
Database: PDB / ID: 2vb8
Titlebeta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
KeywordsTRANSFERASE / CYTOPLASM / ANTIBIOTIC / THIOLACTOMYCIN / ACYLTRANSFERASE / LIPID SYNTHESIS / FATTY ACID SYNTHESIS / FATTY ACID BIOSYNTHESIS
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 / 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 / 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
THIOLACTOMYCIN / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPappenberger, G. / Schulz-Gasch, T. / Bailly, J. / Hennig, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure-Assisted Discovery of an Aminothiazole Derivative as a Lead Molecule for Inhibition of Bacterial Fatty-Acid Synthesis.
Authors: Pappenberger, G. / Schulz-Gasch, T. / Kusznir, E. / Mueller, F. / Hennig, M.
History
DepositionSep 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 1
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,53710
Polymers170,6254
Non-polymers9126
Water47,6502645
1
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8046
Polymers85,3122
Non-polymers4914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-52.9 kcal/mol
Surface area29760 Å2
MethodPQS
2
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7334
Polymers85,3122
Non-polymers4212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-42.8 kcal/mol
Surface area29590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.139, 138.345, 211.968
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 1 / 3-OXOACYL- [ACYL-CARRIER-PROTEIN] SYNTHASE I / BETA-KETOACYL-ACP SYNTHASE I / KAS I


Mass: 42656.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-TLM / THIOLACTOMYCIN / 4-HYDROXY-3,5-DIMETHYL-5-(2-METHYL-BUTA-1,3-DIENYL)-5H-THIOPHEN-2-ONE


Mass: 210.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14O2S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2645 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5; SOAK WITH 0.3MM LIGAND IN 2.3M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9511
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 515847 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.51 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK4

1ek4


Resolution: 1.52→119.52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.222 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 13446 5 %RANDOM
Rwork0.151 ---
obs0.153 253711 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.52→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11748 0 58 2645 14451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212243
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.96116517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89851610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56324.289485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.244152093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1641568
X-RAY DIFFRACTIONr_chiral_restr0.1010.21851
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.26866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.28677
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.22289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.2133
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.21568122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.766912658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.18364567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.56493859
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 963
Rwork0.259 17475

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