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- PDB-5ab5: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

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Basic information

Entry
Database: PDB / ID: 5ab5
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) form-II.
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
Nonspecific lipid-transfer protein, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98115
Polymers90,7322
Non-polymers1,24913
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-193.1 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.689, 66.689, 157.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4979, -0.8672, -0.002531), (-0.8672, 0.4979, -5.1E-5), (0.001304, 0.002169, -1)
Vector: 133.3, 77.18, 9.747)

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Components

#1: Protein SCP2-THIOLASE LIKE PROTEIN


Mass: 45365.898 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 47.1 % / 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
Reflection twinOperator: H,-H-K,-L L / Fraction: 0.5
ReflectionResolution: 2→28.88 Å / Num. obs: 52628 / % possible obs: 99.8 % / Observed criterion σ(I): 1.3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.3 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.877 Å / σ(F): 1.96 / Phase error: 30.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2204 2554 4.9 %
Rwork0.1981 --
obs0.1996 52602 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 65 119 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036244
X-RAY DIFFRACTIONf_angle_d0.8928480
X-RAY DIFFRACTIONf_dihedral_angle_d12.8222248
X-RAY DIFFRACTIONf_chiral_restr0.057948
X-RAY DIFFRACTIONf_plane_restr0.0041108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.03880.39991570.35192767X-RAY DIFFRACTION94
2.0388-2.08040.32461390.32862796X-RAY DIFFRACTION94
2.0804-2.12560.35081330.30492706X-RAY DIFFRACTION94
2.1256-2.1750.28381520.30542794X-RAY DIFFRACTION94
2.175-2.22940.29731520.28962785X-RAY DIFFRACTION94
2.2294-2.28960.3741380.26952775X-RAY DIFFRACTION95
2.2896-2.35690.25271290.26982775X-RAY DIFFRACTION95
2.3569-2.43290.25661570.26482746X-RAY DIFFRACTION94
2.4329-2.51970.22331660.2732749X-RAY DIFFRACTION94
2.5197-2.62040.24691640.25772775X-RAY DIFFRACTION94
2.6204-2.73950.33181240.24142784X-RAY DIFFRACTION96
2.7395-2.88360.28361440.22972838X-RAY DIFFRACTION95
2.8836-3.06380.24821200.22632780X-RAY DIFFRACTION96
3.0638-3.29960.22231240.20032814X-RAY DIFFRACTION96
3.2996-3.63030.22871310.17272793X-RAY DIFFRACTION95
3.6303-4.15250.14771390.14372783X-RAY DIFFRACTION94
4.1525-5.21980.17111270.13352778X-RAY DIFFRACTION95
5.2198-21.83040.15571550.15482773X-RAY DIFFRACTION94

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