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- PDB-5ab6: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

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Basic information

Entry
Database: PDB / ID: 5ab6
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) in complex with acetoacetyl-CoA.
ComponentsSCP2-THIOLASE LIKE PROTEIN
KeywordsTRANSPORT PROTEIN / COENZYME A / TRYPANOSOMA BRUCEI / SCP2-THIOLASE / SCP2-THIOLASE- LIKE PROTEIN / MALONYL-COA DECARBOXYLASE / GENE KNOCKOUT / LIPID METABOLISM
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Thiolase C-terminal domain-like / Thiolase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / Nonspecific lipid-transfer protein, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarijan, R.K. / Kiema, T.R. / Wierenga, R.K.
CitationJournal: Proteins / Year: 2016
Title: The Scp2-Thiolase-Like Protein (Slp) of Trypanosoma Brucei is an Enzyme Involved in Lipid Metabolism.
Authors: Harijan, R.K. / Mazet, M. / Kiema, T.R. / Bouyssou, G. / Alexson, S.E.H. / Bergmann, U. / Moreau, P. / Michels, P.A.M. / Bringaud, F. / Wierenga, R.K.
History
DepositionAug 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2May 8, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
C: SCP2-THIOLASE LIKE PROTEIN
D: SCP2-THIOLASE LIKE PROTEIN
E: SCP2-THIOLASE LIKE PROTEIN
F: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,36223
Polymers272,1956
Non-polymers6,16617
Water11,638646
1
E: SCP2-THIOLASE LIKE PROTEIN
F: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9159
Polymers90,7322
Non-polymers2,1847
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-60.1 kcal/mol
Surface area26410 Å2
MethodPISA
2
A: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7237
Polymers90,7322
Non-polymers1,9915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-39.5 kcal/mol
Surface area26090 Å2
MethodPISA
3
C: SCP2-THIOLASE LIKE PROTEIN
D: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7237
Polymers90,7322
Non-polymers1,9915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-39.9 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.150, 65.972, 156.755
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA3 - 40819 - 424
21SERSERASPASPBB3 - 40819 - 424
12SERSERASPASPAA3 - 40819 - 424
22SERSERASPASPCC3 - 40819 - 424
13SERSERASPASPAA3 - 40819 - 424
23SERSERASPASPDD3 - 40819 - 424
14GLNGLNASPASPAA4 - 40820 - 424
24GLNGLNASPASPEE4 - 40820 - 424
15SERSERASPASPAA3 - 40819 - 424
25SERSERASPASPFF3 - 40819 - 424
16SERSERASPASPBB3 - 40819 - 424
26SERSERASPASPCC3 - 40819 - 424
17SERSERASPASPBB3 - 40819 - 424
27SERSERASPASPDD3 - 40819 - 424
18GLNGLNASPASPBB4 - 40820 - 424
28GLNGLNASPASPEE4 - 40820 - 424
19SERSERASPASPBB3 - 40819 - 424
29SERSERASPASPFF3 - 40819 - 424
110SERSERASPASPCC3 - 40819 - 424
210SERSERASPASPDD3 - 40819 - 424
111GLNGLNASPASPCC4 - 40820 - 424
211GLNGLNASPASPEE4 - 40820 - 424
112SERSERASPASPCC3 - 40819 - 424
212SERSERASPASPFF3 - 40819 - 424
113GLNGLNASPASPDD4 - 40820 - 424
213GLNGLNASPASPEE4 - 40820 - 424
114SERSERASPASPDD3 - 40819 - 424
214SERSERASPASPFF3 - 40819 - 424
115GLNGLNSERSEREE4 - 40720 - 423
215GLNGLNSERSERFF4 - 40720 - 423

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(-0.9956, -0.09326, -0.003459), (-0.09333, 0.9946, 0.04445), (-0.000705, 0.04458, -0.999)-57.14, -2.731, -0.2406
2given(-0.5511, -0.8344, 0.002536), (0.8339, -0.5509, -0.03306), (0.02898, -0.01611, 0.9995)-75.16, 40.84, -50.93
3given(0.4775, 0.8786, 0.005194), (0.8786, -0.4775, 0.007954), (0.009469, 0.000766, -1)13.9, 42.56, 52.72
4given(0.5528, -0.8333, 0.00145), (-0.833, -0.5526, 0.02606), (-0.02091, -0.01561, -0.9997)-41.3, -7.064, -52.67
5given(-0.4688, 0.8833, -0.001062), (-0.8833, -0.4688, -0.004607), (-0.004567, -0.001221, 1)-15.24, -7.419, 52.32
6given(0.4709, 0.8822, -0.000143), (0.8821, -0.4709, 0.01144), (0.01003, -0.005513, -0.9999)13.91, 42.76, 52.64
7given(-0.5573, -0.8303, -0.00512), (0.8298, -0.5568, -0.0371), (0.02795, -0.02493, 0.9993)-75, 40.78, -51.14
8given(-0.4726, 0.8812, -0.003184), (-0.8811, -0.4726, -0.01881), (-0.01808, -0.006083, 0.9998)-15.33, -8.126, 52.13
9given(0.5495, -0.8355, 0.000832), (-0.8349, -0.549, 0.03993), (-0.03291, -0.02264, -0.9992)-41.31, -6.238, -52.86
10given(0.4699, -0.8824, -0.02515), (-0.8826, -0.4702, 0.007446), (-0.01839, 0.0187, -0.9997)-44.64, -76.93, 103.8
11given(-1, -0.001978, -0.008037), (-0.001982, 1, 0.000533), (0.008036, 0.000549, -1)-58.66, -1.828, -0.06805
12given(-0.4781, -0.8779, 0.02563), (0.878, -0.4785, -0.01257), (0.02329, 0.01649, 0.9996)-70.28, -25.06, 104.9
13given(-0.4682, -0.8835, 0.01411), (0.8835, -0.4684, -0.01185), (0.01707, 0.006917, 0.9998)-70.96, -24.89, 104.7
14given(-0.9999, 0.009738, 0.00489), (0.009748, 1, 0.001958), (-0.004871, 0.002006, -1)-57.83, -1.744, -0.1461
15given(0.4765, 0.879, -0.01755), (0.879, -0.4767, -0.01203), (-0.01894, -0.009689, -0.9998)12.51, -23.15, -104.9

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Components

#1: Protein
SCP2-THIOLASE LIKE PROTEIN


Mass: 45365.898 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: EATRO1125 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZUV7
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.3 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE (PH 4.6), 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2013 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→29.41 Å / Num. obs: 184266 / % possible obs: 98.5 % / Observed criterion σ(I): 2.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.43 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.536 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26422 9153 5 %RANDOM
Rwork0.24762 ---
obs0.24844 174242 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.05 Å2
2--0.39 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17592 0 379 646 18617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01918384
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217552
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.98925006
X-RAY DIFFRACTIONr_angle_other_deg0.884340355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16652366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99523.484706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.808152847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.48215115
X-RAY DIFFRACTIONr_chiral_restr0.0610.22827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120803
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024054
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A244420.05
12B244420.05
21A243290.06
22C243290.06
31A243620.06
32D243620.06
41A244070.05
42E244070.05
51A244940.05
52F244940.05
61B242280.06
62C242280.06
71B243480.06
72D243480.06
81B243630.05
82E243630.05
91B244630.06
92F244630.06
101C240470.07
102D240470.07
111C242100.06
112E242100.06
121C242240.06
122F242240.06
131D242250.06
132E242250.06
141D244730.06
142F244730.06
151E243880.05
152F243880.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 641 -
Rwork0.428 12721 -
obs--97.09 %

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