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- PDB-4b3h: Crystal structure of Mycobacterium tuberculosis fatty acid beta- ... -

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Basic information

Entry
Database: PDB / ID: 4b3h
TitleCrystal structure of Mycobacterium tuberculosis fatty acid beta- oxidation complex
Components
  • FATTY ACID BETA-OXIDATION COMPLEX ALPHA-CHAIN FADB
  • FATTY ACID BETA-OXIDATION COMPLEX BETA-CHAIN FADA
KeywordsOXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE-TRANSFERASE COMPLEX / TFE / TRIFUNCTIONAL ENZYME / HETERO TETRAMER / COA
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
Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVenkatesan, R. / Wierenga, R.
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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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)244,64343
Polymers240,9324
Non-polymers3,71139
Water18,4831026
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18610 Å2
ΔGint-365.1 kcal/mol
Surface area82710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.460, 134.250, 118.400
Angle α, β, γ (deg.)90.00, 110.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2175-

HOH

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Components

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


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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: 3.85 Å3/Da / Density % sol: 68.1 % / Description: NONE
Crystal growpH: 8.5 / Details: 2 M AMMONIUM SULPHATE, 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 CCD / Detector: CCD / Date: Jun 17, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 153278 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDK

1wdk


Resolution: 2.3→49.94 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.206 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22417 8109 5 %RANDOM
Rwork0.19544 ---
obs0.19687 153278 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.78 Å2
2--0.28 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16693 0 204 1026 17923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.98323476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73652298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6524.397680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.556152860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2515105
X-RAY DIFFRACTIONr_chiral_restr0.0670.22691
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112945
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 627 -
Rwork0.266 11104 -
obs--99.99 %
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)
10.0825-0.0356-0.00130.55080.39010.2878-0.00560.0112-0.0192-0.0382-0.02490.046-0.0267-0.02640.03050.0092-0.00920.00340.05250.00770.0303-57.507330.4187-42.4095
20.05880.0524-0.03160.31130.2320.3301-0.00390.0008-0.0056-0.00150.02270.0054-0.0217-0.0348-0.01880.01970.01710.00440.06440.04070.0296-51.52638.184540.2435
30.254-0.01820.23470.364-0.00240.5169-0.03430.0007-0.00380.01270.0291-0.0036-0.02430.00960.00520.02130.00830.00140.02510.02650.0362-24.165549.5893-3.5237
40.25440.138-0.09730.41190.01750.5617-0.04020.0001-0.0586-0.01370.0274-0.02230.01940.01360.01280.02970.00240.00350.0090.01630.0555-25.201117.2605-3.0693
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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