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Yorodumi- PDB-8axo: Crystal structure of the C-terminal domain of Trypanosoma brucei ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8axo | ||||||
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Title | Crystal structure of the C-terminal domain of Trypanosoma brucei CFAP410 | ||||||
Components | TbCFAP410-CTD | ||||||
Keywords | STRUCTURAL PROTEIN / Cilia / Flagella / Coiled-coil | ||||||
Function / homology | Leucine-rich repeat / Leucine-rich repeat profile. / Leucine-rich repeat / cilium / Leucine-rich repeat domain superfamily / Leucine-rich repeat protein (LRRP) Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei TREU927 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.29 Å | ||||||
Authors | Dong, G. / Stadler, A. | ||||||
Funding support | Austria, 1items
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Citation | Journal: To Be Published Title: Structural studies of cilia and flagella associated protein 410 (CFAP410) reveal its bimodular organization with an N-terminal LRR motif and a C-terminal tetrameric helical bundle Authors: Dong, G. / Stadler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8axo.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8axo.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 8axo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/8axo ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8axo | HTTPS FTP |
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-Related structure data
Related structure data | 8axjC 8axrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.414888869432, -0.817997484866, -0.398431099156), (-0.816003137042, -0.528227217356, 0.234765600509), (-0.402499821565, 0.227719392229, -0.886644106755)Vector: -20. ...NCS oper: (Code: given Matrix: (0.414888869432, -0.817997484866, -0.398431099156), Vector: |
-Components
#1: Protein/peptide | Mass: 3913.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote) Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38DI2 #2: 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: 1.86 Å3/Da / Density % sol: 33.85 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / Details: 2.0 M ammonium sulfate, 5% (v/v) iso-propanol / PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→19.1 Å / Num. obs: 15025 / % possible obs: 99.65 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.046 / Rrim(I) all: 0.14 / Net I/σ(I): 8.16 |
Reflection shell | Resolution: 1.29→1.34 Å / Num. unique obs: 1430 / CC1/2: 0.43 / CC star: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.29→19.1 Å / SU ML: 0.1764 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.4872 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→19.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.602751331809 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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