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- PDB-2qx1: Crystal structure of the complex between mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 2qx1
TitleCrystal structure of the complex between mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III (FABH) and decyl-COA disulfide
ComponentsBeta-ketoacyl-ACP synthase III
KeywordsTRANSFERASE / FATTY ACID BIOSYNTHESIS / MYOBACTERIUM TUBERCULOSIS / STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY / ENZYME INHIBITOR COMPLEX / MECHANISM BASED INHIBITOR / 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
COENZYME A / 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: 2.6 Å
AuthorsSachdeva, S. / Musayev, F. / Alhamadsheh, M. / Scarsdale, J.N. / Wright, H.T. / Reynolds, K.A.
Citation
Journal: Bioorg.Chem. / Year: 2008
Title: Probing reactivity and substrate specificity of both subunits of the dimeric Mycobacterium tuberculosis FabH using alkyl-CoA disulfide inhibitors and acyl-CoA substrates
Authors: Sachdeva, S. / Musayev, F. / Alhamadsheh, M.M. / Neel Scarsdale, J. / Tonie Wright, H. / Reynolds, K.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the mycobacterium beta-keto-acyl acyl carrier protein synthase III
Authors: Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a substrate complex of mycobacterium tuberculosis beta-keto-acyl acyl carrier protein synthase III (FABH) with lauroyl coenzyme A
Authors: Musayev, F. / Sachdeva, S. / Scarsdale, J.N. / Reynolds, K.A. / Wright, H.T.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Aug 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 1.4Oct 9, 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: Beta-ketoacyl-ACP synthase III
B: Beta-ketoacyl-ACP synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9235
Polymers69,8072
Non-polymers1,1163
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-39.1 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.649, 89.365, 232.006
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 Beta-ketoacyl-ACP synthase III / 3-oxoacyl- [acyl-carrier-protein] synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / KAS ...3-oxoacyl- [acyl-carrier-protein] synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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.: 145 / 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: 2.46 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100MM NA HEPES, 18% PEG-10K(W.V), pH 7.00, 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: Mar 8, 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: 2.6→39.5 Å / Num. all: 22144 / Num. obs: 21693 / % possible obs: 98 % / Redundancy: 2.76 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2176 / % possible all: 99.9

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Processing

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

1hzp


Resolution: 2.6→14.88 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.822 / SU B: 30.633 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS AND REFMAC WERE USED FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.3162 2178 10.1 %RANDOM
Rwork0.24214 ---
obs0.24951 19381 97.5 %-
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: 29.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---1.25 Å20 Å2
3----1.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.6→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 70 145 5087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9696842
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3523.5200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0915745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8821540
X-RAY DIFFRACTIONr_chiral_restr0.0760.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22646
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23504
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2731.53358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48225248
X-RAY DIFFRACTIONr_scbond_it0.70531846
X-RAY DIFFRACTIONr_scangle_it1.1724.51594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 186 -
Rwork0.331 1432 -
obs--99.88 %
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)
10.8531-0.21870.32961.4911-0.37731.65390.01070.02780.02180.147-0.0132-0.11640.01260.18650.0025-0.1675-0.03580.006-0.08360.021-0.092830.524528.048137.3931
21.469-0.01820.520.9882-0.20381.44820.00730.06620.1046-0.11480.01460.1415-0.1143-0.0891-0.0219-0.0860.0042-0.035-0.0872-0.0005-0.05511.02143.390520.8861
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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