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- PDB-4b3j: Crystal structure of Mycobacterium tuberculosis fatty acid beta- ... -

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Basic information

Entry
Database: PDB / ID: 4b3j
TitleCrystal structure of Mycobacterium tuberculosis fatty acid beta- oxidation complex with CoenzymeA bound at the hydratase and thiolase active sites
Components(FATTY ACID BETA-OXIDATION COMPLEX ...) x 2
KeywordsOXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE-TRANSFERASE COMPLEX / TFE / TRIFUNCTIONAL ENZYME / HYDRATASE
Function / homology
Function and homology information


long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / acetyl-CoA C-acetyltransferase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / : / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. ...N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / : / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / COENZYME A / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsVenkatesan, R. / Wierenga, R.K.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Structure of Mycobacterial Beta-Oxidation Trifunctional Enzyme Reveals its Altered Assembly and Putative Substrate Channeling Pathway.
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionJul 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID BETA-OXIDATION COMPLEX ALPHA-CHAIN FADB
B: FATTY ACID BETA-OXIDATION COMPLEX ALPHA-CHAIN FADB
C: FATTY ACID BETA-OXIDATION COMPLEX BETA-CHAIN FADA
D: FATTY ACID BETA-OXIDATION COMPLEX BETA-CHAIN FADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,99943
Polymers240,9324
Non-polymers7,06739
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23050 Å2
ΔGint-316.3 kcal/mol
Surface area81670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.300, 135.250, 118.580
Angle α, β, γ (deg.)90.00, 110.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-1408-

SO4

21C-2150-

HOH

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Components

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FATTY ACID BETA-OXIDATION COMPLEX ... , 2 types, 4 molecules ABCD

#1: Protein FATTY ACID BETA-OXIDATION COMPLEX ALPHA-CHAIN FADB / ENOYLCOA HYDRATASE / HYDROXYACYLCOA DEHYDROGENASE / PROBABLE FATTY OXIDATION PROTEIN FADB


Mass: 78005.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET DUET, PACYC DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS
References: UniProt: O53872, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein FATTY ACID BETA-OXIDATION COMPLEX BETA-CHAIN FADA / THIOLASE / PUTATIVE ACYLTRANSFERASE RV0859


Mass: 42460.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET DUET, PACYC DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: O53871, acetyl-CoA C-acetyltransferase

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Non-polymers , 5 types, 876 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details16 RESIDUES EXTRA AT THE N-TERMINUS INCLUDING HISTINE TAG

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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: 3.87 Å3/Da / Density % sol: 68.25 % / Description: NONE
Crystal growpH: 8.5 / Details: 2 M AMMONIUM SULFATE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.5→49.35 Å / Num. obs: 119944 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→48.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.401 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 6303 5 %RANDOM
Rwork0.18133 ---
obs0.18333 119944 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.528 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20.62 Å2
2---0.02 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16690 0 418 837 17945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.99823905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.06952309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0124.381687
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.666152869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.67515107
X-RAY DIFFRACTIONr_chiral_restr0.0790.22719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113102
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 442 -
Rwork0.262 8722 -
obs--99.85 %
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)
10.09240.05850.04290.58460.41770.3034-0.0376-0.0094-0.0213-0.0656-0.0040.0603-0.043-0.01810.04160.0228-0.0099-0.00160.04760.0120.0372-57.444130.6698-42.3606
20.05650.00970.0140.30570.29760.3716-0.018-0.0163-0.01220.00110.02370.0266-0.0106-0.0499-0.00570.01350.00820.00020.07570.04090.027-51.42938.491240.3566
30.34160.01270.12410.31650.13930.4776-0.02360.02080.01080.00580.0174-0.0005-0.00330.02030.00620.01480.00860.00280.02320.02840.0471-24.301749.9278-3.3017
40.22970.054-0.03110.37440.08090.4995-0.0149-0.0099-0.0486-0.00970.0025-0.03090.03260.00190.01240.02420.0006-0.00490.00550.0180.0681-25.065917.5895-2.9475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-13 - 720
2X-RAY DIFFRACTION2B-14 - 720
3X-RAY DIFFRACTION3C2 - 403
4X-RAY DIFFRACTION4D1 - 403

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