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

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Basic information

Entry
Database: PDB / ID: 2vba
Titlebeta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
KeywordsTRANSFERASE / CYTOPLASM / ANTIBIOTIC / AMINO-THIAZOLE / 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, 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 / 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
2-PHENYLAMINO-4-METHYL-5-ACETYL THIAZOLE / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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)170,8575
Polymers170,6254
Non-polymers2321
Water43,7942431
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)85,5453
Polymers85,3122
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-44.4 kcal/mol
Surface area30090 Å2
MethodPQS
2
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1


Theoretical massNumber of molelcules
Total (without water)85,3122
Polymers85,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-41.2 kcal/mol
Surface area29810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.950, 139.480, 212.170
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 / BETA-KETOACYL-ACP SYNTHASE I / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] 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-P4T / 2-PHENYLAMINO-4-METHYL-5-ACETYL THIAZOLE / 1-[4-methyl-2-(phenylamino)-1,3-thiazol-5-yl]ethanone


Mass: 232.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2431 / 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 0.01M LIGAND IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 0.005M TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97881
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 1.36→20 Å / Num. obs: 685131 / % possible obs: 92.3 % / Observed criterion σ(I): 5 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.2 / % possible all: 72.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK4

1ek4


Resolution: 1.36→19.87 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.18 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.151 17776 5 %RANDOM
Rwork0.119 ---
obs0.121 337314 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.36→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11768 0 16 2431 14215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212150
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.95616413
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46124.336482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.162152030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0451566
X-RAY DIFFRACTIONr_chiral_restr0.1040.21859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029120
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.26349
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28656
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.22003
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.293
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3310.678111
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.184112679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8760.674466
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.91213734
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: 1.36→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.187 929
Rwork0.131 17788

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