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- PDB-2qo1: 2.6 Angstrom Crystal Structure of the Complex Between 11-(decyldi... -

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Basic information

Entry
Database: PDB / ID: 2qo1
Title2.6 Angstrom Crystal Structure of the Complex Between 11-(decyldithiocarbonyloxy)-undecanoic acid and Mycobacterium Tuberculosis FabH.
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / FATTY ACID BIOSYNTHESIS / MYOBACTERIUM TUBERCULOSIS / STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY / ENZYME INHIBITOR COMPLEX / MECHANISM BASED INHIBITOR / SUBSTRATE ENTRY AND EXIT / Acyltransferase / 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 / 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 / 11-[(MERCAPTOCARBONYL)OXY]UNDECANOIC ACID / 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: 2.6 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: Muysavev, 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: Advisory / 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 1.4Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)70,6806
Polymers69,8072
Non-polymers8734
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.411, 89.123, 233.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 34903.391 Da / Num. of mol.: 2
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-VZZ / 11-[(MERCAPTOCARBONYL)OXY]UNDECANOIC ACID


Mass: 262.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22O4S
#3: Chemical ChemComp-D1T / DECANE-1-THIOL


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M NA/K TARTATE, 100MM NA HEPES BUFFER, pH 7.50, 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: Jul 7, 2006 / Details: RIGAKU VARIMAX CONFOCAL OPTICS
RadiationMonochromator: RIGAKU VARIMAX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→39.73 Å / Num. all: 22465 / Num. obs: 20938 / % possible obs: 93.2 % / Redundancy: 2.54 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2219 / Rsym value: 0.24 / % possible all: 98.8

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Processing

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

1hzp


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.823 / SU B: 26.637 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS AND REFMAC WERE USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29801 2076 10 %RANDOM
Rwork0.22105 ---
obs0.22865 20783 93.24 %-
all-22289 --
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: 40.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.76 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 56 138 4999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9626718
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02523.386189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23115711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3521539
X-RAY DIFFRACTIONr_chiral_restr0.070.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22606
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23445
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.261.53364
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45125231
X-RAY DIFFRACTIONr_scbond_it0.58731747
X-RAY DIFFRACTIONr_scangle_it0.9454.51487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 146 -
Rwork0.287 1459 -
obs--98.89 %
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)
11.01960.46810.33881.6725-0.37761.30160.0423-0.1569-0.04960.1012-0.1305-0.2260.01520.13350.0882-0.17680.0672-0.0309-0.11420.0049-0.042130.984928.206737.5914
22.00930.41920.87951.32950.121.6252-0.1850.05870.229-0.13810.04190.0803-0.2485-0.12030.1431-0.09990.0961-0.0347-0.1307-0.0156-0.085211.9843.341820.918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 31711 - 332
2X-RAY DIFFRACTION2BB1 - 31711 - 332

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