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- PDB-4ubu: Structure of a modified C93S variant of the 3-ketoacyl-CoA thiola... -

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Basic information

Entry
Database: PDB / ID: 4ubu
TitleStructure of a modified C93S variant of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis in complex with CoA
ComponentsAcetyl-CoA acetyltransferase FadA5
KeywordsTRANSFERASE / acetylated / degradative thiolase
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 / 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
COENZYME A / Steroid 3-ketoacyl-CoA thiolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchaefer, C.M. / Kisker, C.
Funding support Germany, United States, 8items
OrganizationGrant numberCountry
German Research FoundationFZ82 Germany
German Research FoundationSFB630 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 2.0Oct 2, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_assembly
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 / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_details
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

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase FadA5
B: Acetyl-CoA acetyltransferase FadA5
C: Acetyl-CoA acetyltransferase FadA5
D: Acetyl-CoA acetyltransferase FadA5
E: Acetyl-CoA acetyltransferase FadA5
F: Acetyl-CoA acetyltransferase FadA5
G: Acetyl-CoA acetyltransferase FadA5
H: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,49020
Polymers338,9828
Non-polymers6,50912
Water70339
1
G: Acetyl-CoA acetyltransferase FadA5
hetero molecules

E: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5577
Polymers84,7452
Non-polymers1,8115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
2
E: Acetyl-CoA acetyltransferase FadA5
hetero molecules

G: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5577
Polymers84,7452
Non-polymers1,8115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
3
A: Acetyl-CoA acetyltransferase FadA5
D: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2804
Polymers84,7452
Non-polymers1,5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-16 kcal/mol
Surface area26060 Å2
MethodPISA
4
B: Acetyl-CoA acetyltransferase FadA5
C: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2804
Polymers84,7452
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-16 kcal/mol
Surface area26060 Å2
MethodPISA
5
F: Acetyl-CoA acetyltransferase FadA5
H: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3735
Polymers84,7452
Non-polymers1,6273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-15 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.610, 105.160, 147.660
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
31B
41C
51D
61E
71F
81G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 391
2111H1 - 391
3111B1 - 391
4111C1 - 391
5111D1 - 391
6111E1 - 391
7111F1 - 391
8111G1 - 391
1211A400
2211H400
3211B400
4211C400
5211D400
6211E400
7211F400
8211G400

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999626, 0.024983, 0.011138), (-0.023936, -0.996013, 0.085934), (0.013241, 0.085636, 0.996239)24.28132, 39.89096, -72.57516
3given(-0.98496, 0.172659, -0.006491), (0.158777, 0.889671, -0.428106), (-0.068142, -0.422698, -0.903705)84.32133, 20.54636, 70.44886
4given(0.999467, -0.009506, -0.031231), (0.012162, 0.996221, 0.085994), (0.030295, -0.086328, 0.995806)-39.49842, -6.35248, -69.24789
5given(-0.984635, 0.167008, -0.051006), (0.170121, 0.851522, -0.495953), (-0.039395, -0.49701, -0.86685)42.63779, -2.24216, 5.90636
6given(-0.998568, 0.033482, -0.041716), (-0.040178, -0.984324, 0.171735), (-0.035312, 0.173165, 0.98426)110.21055, 49.85165, 0.39465
7given(0.981634, -0.184084, -0.050077), (-0.187664, -0.884576, -0.426974), (0.034302, 0.42853, -0.902876)28.96803, 72.19288, 47.61163
8given(-0.981601, -0.190049, -0.018489), (0.17097, -0.917896, 0.358101), (-0.085027, 0.348351, 0.9335)57.04838, -12.82304, 5.79017

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Components

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


Mass: 42372.695 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
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
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Mes, 1.8 M (NH4)2SO4, 10% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→58.75 Å / Num. obs: 70941 / % possible obs: 95 % / Redundancy: 2 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 4.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.3 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ubv

4ubv


Resolution: 3→58.82 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.802 / SU B: 44.471 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28728 3551 5 %RANDOM
Rwork0.2475 ---
obs0.24952 67371 94.68 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 43.948 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å2-0 Å21.25 Å2
2--2.25 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 3→58.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23260 0 408 39 23707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01924123
X-RAY DIFFRACTIONr_bond_other_d0.0030.0223244
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.97232779
X-RAY DIFFRACTIONr_angle_other_deg0.849353201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36853146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38923.7391035
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8153867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0215222
X-RAY DIFFRACTIONr_chiral_restr0.0760.23726
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227852
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025432
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
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5734 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.67
H7.89
B5
C6.06
D5.62
E6.3
F5.54
G4.9
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 265 -
Rwork0.322 4925 -
obs--94.66 %
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)
11.3717-0.13280.4750.88930.30161.1686-0.0034-0.0560.00940.0785-0.0387-0.0429-0.0590.1440.04210.178-0.01820.02480.0895-0.00090.017734.331924.17768.3474
22.1584-0.06620.40.25890.08221.8882-0.14020.2499-0.38010.01640.04950.0245-0.0615-0.08270.09070.1391-0.01840.05360.0547-0.05630.089154.033420.855654.8899
32.4962-0.57440.51411.25340.33671.255-0.2568-0.2196-0.29020.12550.19210.0236-0.10640.14350.06470.20760.02970.05090.07510.04710.065276.51623.013377.5865
42.0449-0.07670.36570.33490.1171.5694-0.01710.2514-0.04170.0023-0.04040.12030.0003-0.06790.05740.1795-0.00490.02680.0583-0.03020.055912.571319.8992-14.7906
52.2544-0.0501-0.90480.7331-0.15081.4342-0.0027-0.1036-0.06090.02750.00110.0272-0.0009-0.08890.00170.1671-0.02440.010.0372-0.00340.007276.526724.13536.5613
62.24621.0415-0.19990.78710.24921.7403-0.11220.27960.0539-0.05960.0897-0.01350.06090.08230.02250.1008-0.01360.00990.05990.01180.036412.938624.652755.6818
72.4665-0.5591-0.76120.540.0721.7012-0.1767-0.3072-0.26020.05920.05670.17160.0283-0.05540.120.1580.03550.0420.05770.02470.064828.4177-28.689115.9886
82.72350.1286-0.66131.3762-0.2191.03330.1984-0.24090.24050.3324-0.24040.12850.0571-0.20040.04190.2273-0.12750.0670.1592-0.08090.0473-8.520622.97779.2693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 391
2X-RAY DIFFRACTION2B1 - 391
3X-RAY DIFFRACTION3C1 - 391
4X-RAY DIFFRACTION4D1 - 391
5X-RAY DIFFRACTION5E0 - 391
6X-RAY DIFFRACTION6F1 - 391
7X-RAY DIFFRACTION7G-1 - 391
8X-RAY DIFFRACTION8H-2 - 391

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