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- PDB-5ab4: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

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Basic information

Entry
Database: PDB / ID: 5ab4
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) form-I.
ComponentsSCP2-THIOLASE LIKE PROTEIN
KeywordsTRANSPORT PROTEIN / COENZYME A / SCP2-THIOLASE / SCP2-THIOLASE-LIKE PROTEIN / MALONYL-COA DECARBOXYLASE / GENE KNOCKOUT / LIPID METABOLISM
Function / homologyThiolase / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta / Nonspecific lipid-transfer protein, putative
Function and homology information
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)90,7322
Polymers90,7322
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-20.1 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.448, 67.448, 157.050
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: (-0.4993, 0.8665, -0.001949), (0.8665, 0.4993, 0.000451), (0.001364, -0.001463, -1)
Vector: -67.43, 38.9, -5.661)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 48.1 % / Description: NONE
Crystal growpH: 5.5
Details: 100 MM SODIUM CITRATE (PH 5.5), 10% (W/V) PEG4000, 200 MM SODIUM ACETATE

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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
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 1.75→46.87 Å / Num. obs: 80250 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZBG

3zbg


Resolution: 1.751→46.867 Å / σ(F): 1.96 / Phase error: 38.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2154 4039 5.1 %
Rwork0.1987 --
obs0.2012 79395 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→46.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 0 0 139 6085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066070
X-RAY DIFFRACTIONf_angle_d1.2068240
X-RAY DIFFRACTIONf_dihedral_angle_d13.922190
X-RAY DIFFRACTIONf_chiral_restr0.072936
X-RAY DIFFRACTIONf_plane_restr0.0051082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7509-1.78110.46072300.43723771X-RAY DIFFRACTION93
1.7811-1.81350.43552020.39063774X-RAY DIFFRACTION94
1.8135-1.84840.37771890.3813722X-RAY DIFFRACTION94
1.8484-1.88610.38821740.37983853X-RAY DIFFRACTION95
1.8861-1.92710.49051920.46353586X-RAY DIFFRACTION89
1.9271-1.97190.35581790.34033705X-RAY DIFFRACTION92
1.9719-2.02120.33771960.32293756X-RAY DIFFRACTION94
2.0212-2.07590.34952020.33863752X-RAY DIFFRACTION94
2.0759-2.1370.34412180.31813786X-RAY DIFFRACTION94
2.137-2.20590.32671990.30033804X-RAY DIFFRACTION94
2.2059-2.28470.33252100.33553623X-RAY DIFFRACTION90
2.2847-2.37620.34252380.29043798X-RAY DIFFRACTION94
2.3762-2.48430.28321910.28423792X-RAY DIFFRACTION95
2.4843-2.61520.27481790.27373828X-RAY DIFFRACTION95
2.6152-2.7790.24911900.24583798X-RAY DIFFRACTION95
2.779-2.99340.22721940.2333810X-RAY DIFFRACTION95
2.9934-3.29440.19332230.19443780X-RAY DIFFRACTION94
3.2944-3.77050.17922070.14973846X-RAY DIFFRACTION94
3.7705-4.74810.13682080.11263785X-RAY DIFFRACTION94
4.7481-32.5910.14651920.11923797X-RAY DIFFRACTION95

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