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- PDB-5ab7: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

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Basic information

Entry
Database: PDB / ID: 5ab7
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) in complex with malonyl-CoA.
ComponentsSCP2-THIOLASE LIKE PROTEIN
KeywordsTRANSPORT PROTEIN / COENZYME A / 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
MALONYL-COENZYME A / Nonspecific lipid-transfer protein, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2, 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)278,66226
Polymers272,1956
Non-polymers6,46620
Water5,296294
1
A: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7277
Polymers90,7322
Non-polymers1,9955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-80 kcal/mol
Surface area26240 Å2
MethodPISA
2
C: SCP2-THIOLASE LIKE PROTEIN
D: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,01510
Polymers90,7322
Non-polymers2,2848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-118.8 kcal/mol
Surface area26410 Å2
MethodPISA
3
E: SCP2-THIOLASE LIKE PROTEIN
F: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9199
Polymers90,7322
Non-polymers2,1877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-106.1 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.546, 66.404, 159.834
Angle α, β, γ (deg.)90.00, 91.18, 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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA3 - 40819 - 424
21ASPASPBB3 - 40819 - 424
12LEULEUAA3 - 40919 - 425
22LEULEUCC3 - 40919 - 425
13LEULEUAA3 - 40919 - 425
23LEULEUDD3 - 40919 - 425
14LEULEUAA3 - 40919 - 425
24LEULEUEE3 - 40919 - 425
15LEULEUAA3 - 40919 - 425
25LEULEUFF3 - 40919 - 425
16SERSERBB3 - 40719 - 423
26SERSERCC3 - 40719 - 423
17ASPASPBB3 - 40819 - 424
27ASPASPDD3 - 40819 - 424
18ASPASPBB3 - 40819 - 424
28ASPASPEE3 - 40819 - 424
19ASPASPBB3 - 40819 - 424
29ASPASPFF3 - 40819 - 424
110LEULEUCC3 - 40919 - 425
210LEULEUDD3 - 40919 - 425
111LEULEUCC3 - 40919 - 425
211LEULEUEE3 - 40919 - 425
112LEULEUCC3 - 40919 - 425
212LEULEUFF3 - 40919 - 425
113LEULEUDD3 - 40919 - 425
213LEULEUEE3 - 40919 - 425
114LEULEUDD3 - 40919 - 425
214LEULEUFF3 - 40919 - 425
115LEULEUEE3 - 40919 - 425
215LEULEUFF3 - 40919 - 425

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

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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-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.4 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: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→29.38 Å / Num. obs: 104486 / % possible obs: 95.3 % / Observed criterion σ(I): 1.9 / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.9 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.4 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.317 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.474 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24887 5191 5 %RANDOM
Rwork0.23589 ---
obs0.23655 98670 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.176 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-0.39 Å2
2--1.16 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17527 0 394 294 18215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01918322
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217458
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9924923
X-RAY DIFFRACTIONr_angle_other_deg0.913340148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1952352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77523.508707
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22152837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.06415114
X-RAY DIFFRACTIONr_chiral_restr0.0550.22818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024038
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)
11A241970.07
12B241970.07
21A243830.06
22C243830.06
31A244280.06
32D244280.06
41A243230.07
42E243230.07
51A242220.07
52F242220.07
61B240720.07
62C240720.07
71B244740.06
72D244740.06
81B240550.07
82E240550.07
91B243310.06
92F243310.06
101C244330.06
102D244330.06
111C242230.07
112E242230.07
121C240190.07
122F240190.07
131D242640.06
132E242640.06
141D244110.07
142F244110.07
151E239890.08
152F239890.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 382 -
Rwork0.355 7065 -
obs--91.95 %

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