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- PDB-4ubv: Structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculos... -

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Basic information

Entry
Database: PDB / ID: 4ubv
TitleStructure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis with an partially acetylated cysteine in complex with acetyl-CoA and CoA
ComponentsAcetyl-CoA acetyltransferase FadA5
KeywordsTRANSFERASE / partially acetylated degradative thiolase / acetyl-CoA / CoA
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / cholesterol catabolic process / fatty acid beta-oxidation / identical protein binding
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / 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, C-terminal / Thiolase, C-terminal domain / Thiolase / 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
ACETYL COENZYME *A / COENZYME A / 1,4-DIETHYLENE DIOXIDE / Steroid 3-ketoacyl-CoA thiolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 8, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_ref_seq_dif / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)89,04827
Polymers84,6932
Non-polymers4,35525
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-13 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.680, 124.680, 124.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-48-

HIS

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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: THE THIOLASE FADA5 IN COMPLEX WITH ACETYL-COA AND COA; THE THIOLASE IS PARTIALLY COVALENTLY MODIFIED AT C93 (ACETYLATED)
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / 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 , 6 types, 306 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Mes pH 6.5, 4% 1,4-dioxane, 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: May 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→35.99 Å / Num. obs: 72009 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALAdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u1q

1u1q


Resolution: 1.95→35.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.58 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 3640 5.1 %RANDOM
Rwork0.19313 ---
obs0.19503 68289 99.97 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 29.824 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å2-0 Å2-0 Å2
2---2.04 Å20 Å2
3---4.08 Å2
Refinement stepCycle: 1 / Resolution: 1.95→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 276 281 6371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3582.0048578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51123.716261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06415991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0381556
X-RAY DIFFRACTIONr_chiral_restr0.1160.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0214658
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 279 -
Rwork0.237 4955 -
obs--100 %
Refinement TLS params.

L13: 0.0427 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°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)
10.5327-0.22521.32620.04661.9041-0.058-0.08480.0450.14630.05790.0101-0.20510.01690.00010.2178-0.0083-0.02860.1390.00710.0097-27.892410.4652-4.1643
20.7850.15371.32880.08691.8328-0.0470.0868-0.0618-0.14260.02050.0260.0265-0.01450.02650.156-0.00320.00140.11530.00810.0086-30.1237-11.1206-27.8657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 391
2X-RAY DIFFRACTION2B0 - 391

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