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- PDB-2qo0: Crystal structure of the complex between the A246F mutant of myco... -

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Entry
Database: PDB / ID: 2qo0
TitleCrystal structure of the complex between the A246F mutant of mycobacterium beta-ketoacyl-acyl carrier protein synthase III (FABH) and 11-(decyldithiocarbonyloxy)-undecanoic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / FATTY ACID BIOSYNTHESIS / MYOBACTERIUM TUBERCULOSIS / STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY / ENZYME INHIBITOR COMPLEX / MECHANISM BASED INHIBITOR / Acyltransferase / Cytoplasm / Lipid synthesis / Multifunctional enzyme
Function / homology
Function and homology information


mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
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
DECANE-1-THIOL / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / Mycobacterial beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSachdeva, S. / Musayev, F. / Alhamadsheh, M. / Scarsdale, J.N. / Wright, H.T. / Reynolds, K.A.
Citation
Journal: Chem.Biol. / Year: 2008
Title: Separate Entrance and Exit Portals for Ligand Traffic in Mycobacterium tuberculosis FabH
Authors: Sachdeva, S. / Musayev, F.N. / Alhamadsheh, M.M. / Scarsdale, J.N. / Wright, H.T. / Reynolds, K.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of the Mycobacterium Tuberculosis Beta-Ketoacyl-Acy; Carrier Protein Synthase III
Authors: Musayev, F. / Sachdeva, S. / Scarsdale, J.N. / Reynolds, K.A. / Wright, H.T.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of a Substrate Complex of Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Sythnase III (FABH) with Lauroyl-Coenzyme A.
Authors: Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T.
History
DepositionJul 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,3084
Polymers69,9592
Non-polymers3492
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.301, 93.052, 104.722
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 3 / 3-oxoacyl- [acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III / MtFabH


Mass: 34979.484 Da / Num. of mol.: 2 / Mutation: A246F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fabH / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-D1T / DECANE-1-THIOL


Mass: 174.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.87 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100MM NA CITRATE, PH 5.60, 10% ISOPROPANOL, 18% PEG-4K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2006 / Details: RIGAKU VARIMAX CONFOCAL OPTICS
RadiationMonochromator: RIGAKU VARIMAX CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→38.02 Å / Num. all: 46962 / Num. obs: 46884 / % possible obs: 99.8 % / Redundancy: 6.37 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.17 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 4614 / Rsym value: 0.314 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZP

1hzp


Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.962 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26396 4710 10.1 %RANDOM
Rwork0.19423 ---
obs0.20125 46774 99.78 %-
all-46877 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.898 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2--1.65 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 22 320 5153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9566707
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29123.454194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47215717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9441539
X-RAY DIFFRACTIONr_chiral_restr0.0810.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22565
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23441
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2455
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.86543344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.92165229
X-RAY DIFFRACTIONr_scbond_it8.49281733
X-RAY DIFFRACTIONr_scangle_it9.897101478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 368 -
Rwork0.314 3050 -
obs--99.85 %

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