+Open data
-Basic information
Entry | Database: PDB / ID: 5kmx | ||||||
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Title | Structure of Trypanosoma congolense Insect Stage Antigen | ||||||
Components | (Putative uncharacterized protein TCIL3000_10_9440) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / Bi-lobed architecture / surface protein / putative sensor | ||||||
Function / homology | Extensin domain / Extensin-like region / structural constituent of cell wall / membrane => GO:0016020 / Uncharacterized protein TCIL3000_10_9440 Function and homology information | ||||||
Biological species | Trypanosoma congolense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å | ||||||
Model details | Bi-lobed protein | ||||||
Authors | Ramaswamy, R. / Parker, M.L. / Boulanger, M.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Protein Sci. / Year: 2016 Title: Structural characterization reveals a novel bilobed architecture for the ectodomains of insect stage expressed Trypanosoma brucei PSSA-2 and Trypanosoma congolense ISA. Authors: Ramaswamy, R. / Goomeshi Nobary, S. / Eyford, B.A. / Pearson, T.W. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kmx.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kmx.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kmx_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 5kmx_full_validation.pdf.gz | 491.4 KB | Display | |
Data in XML | 5kmx_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 5kmx_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/5kmx ftp://data.pdbj.org/pub/pdb/validation_reports/km/5kmx | HTTPS FTP |
-Related structure data
Related structure data | 5klhSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Details | Monomer as determined by size exclusion chromatography. |
-Components
#1: Protein | Mass: 26145.184 Da / Num. of mol.: 4 / Fragment: residues 40-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_9440 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G0UXP9 #2: Protein/peptide | | Mass: 1209.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_9440 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.85 Å3/Da / Density % sol: 56.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 20% PEG 3350 with 0.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014 / Details: Rh coated flat, toroidal focusing |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→39.472 Å / Num. obs: 42706 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.65 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.452→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.821 / % possible all: 98.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KLH Resolution: 2.452→39.472 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.95 Å2 / Biso mean: 64.65 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.452→39.472 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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