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Yorodumi- PDB-5ab5: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ab5 | ||||||
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Title | Crystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) form-II. | ||||||
Components | SCP2-THIOLASE LIKE PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / COENZYME A / SCP2-THIOLASE / SCP2-THIOLASE-LIKE PROTEIN / MALONYL-COA DECARBOXYLASE / GENE KNOCKOUT / LIPID METABOLISM | ||||||
Function / homology | Thiolase / 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 species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Harijan, R.K. / Kiema, T.R. / Wierenga, R.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ab5.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ab5.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ab5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ab5_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
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Full document | 5ab5_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 5ab5_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 5ab5_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5ab5 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5ab5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4979, -0.8672, -0.002531), Vector: |
-Components
#1: 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 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.1 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE (PH 4.6), 2.0 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection twin | Operator: H,-H-K,-L L / Fraction: 0.5 |
Reflection | Resolution: 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 shell | Resolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.877 Å / σ(F): 1.96 / Phase error: 30.58 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.877 Å
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Refine LS restraints |
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LS refinement shell |
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