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- PDB-4ubw: Apo structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberc... -

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Basic information

Entry
Database: PDB / ID: 4ubw
TitleApo structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis
ComponentsAcetyl-CoA acetyltransferase FadA5
KeywordsTRANSFERASE / degradative thiolase / apo / Mycobacterium tuberculosis / cholesterol metabolism
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation / cholesterol catabolic process / identical protein binding
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Steroid 3-ketoacyl-CoA thiolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchaefer, C.M. / Kisker, C.
Funding support Germany, United States, 8items
OrganizationGrant numberCountry
German Research FoundationSFB630 Germany
German Research FoundationFZ82 Germany
National Institutes of HealthAI092455 United States
National Institutes of HealthAI085349 United States
National Institutes of HealthAI065251 United States
National Institutes of HealthHL53306 United States
National Institutes of HealthRR021008 United States
NSFBIO1039771 United States
CitationJournal: Structure / Year: 2015
Title: FadA5 a Thiolase from Mycobacterium tuberculosis: A Steroid-Binding Pocket Reveals the Potential for Drug Development against Tuberculosis.
Authors: Schaefer, C.M. / Lu, R. / Nesbitt, N.M. / Schiebel, J. / Sampson, N.S. / Kisker, C.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase FadA5
B: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33636
Polymers84,6932
Non-polymers2,64234
Water2,900161
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint9 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.250, 128.250, 114.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetyl-CoA acetyltransferase FadA5 / Probable acetyl-CoA acetyltransferase FadA5 (Acetoacetyl-CoA thiolase)


Mass: 42346.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: apo structure of FadA5 / Source: (gene. exp.) Mycobacterium tuberculosis H37Rv / Gene: fadA5, Rv3546, P425_03688, RVBD_3546 / Plasmid: pSD31
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I6XHI4

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Non-polymers , 5 types, 195 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M Mes pH 6.1, 5% DMSO, 1.8 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→52.02 Å / Num. obs: 25129 / % possible obs: 94.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ubv

4ubv


Resolution: 2.7→51.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 23.376 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24808 1264 5 %RANDOM
Rwork0.17112 ---
obs0.17508 23813 93.72 %-
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: 42.358 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å2-0 Å2
2---1.52 Å20 Å2
3---3.04 Å2
Refinement stepCycle: 1 / Resolution: 2.7→51.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 142 161 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196085
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.968238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4145812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48223.435262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47715987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6271560
X-RAY DIFFRACTIONr_chiral_restr0.1090.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214586
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_it1.8363.0493156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0344.5663955
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2053.4752928
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.44825.7429661
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 106 -
Rwork0.246 1601 -
obs--88.13 %
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)
10.7019-0.04490.1040.2311-0.11141.2870.0786-0.07570.0364-0.0116-0.09060.03690.0809-0.10030.01210.0238-0.0085-0.02390.0827-0.04020.0818-12.196436.2156-3.0468
20.8540.00620.2960.21290.36271.27750.14210.1520.03260.0246-0.0621-0.03190.06150.1107-0.08010.04460.027-0.01920.1093-0.01110.066310.740333.3376-26.1319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 391
2X-RAY DIFFRACTION2B1 - 391

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