+Open data
-Basic information
Entry | Database: PDB / ID: 5jir | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Treponema pallidum protein Tp0624 | ||||||
Components | OOP family OmpA-OmpF porin | ||||||
Keywords | UNKNOWN FUNCTION / OmpA-like / peptidoglycan / modular assembly / neofunctionalized | ||||||
Function / homology | OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Treponema pallidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Parker, M.L. / Boulanger, M.J. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Plos One / Year: 2016 Title: The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains. Authors: Parker, M.L. / Houston, S. / Wetherell, C. / Cameron, C.E. / Boulanger, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jir.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jir.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jir_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jir_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 5jir_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5jir_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jir ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jir | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46741.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema pallidum (strain Nichols) (bacteria) Strain: Nichols / Gene: TP_0624, TPANIC_0624 / Production host: Escherichia coli (E. coli) / References: UniProt: O83632 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 M Hepes pH 6.8, 0.25 M MgCl2, 14% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2013 |
Radiation | Monochromator: ACCEL/BRUKER double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→63.02 Å / Num. obs: 101666 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.7→51.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.19
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.79 Å2 / Biso mean: 28.1832 Å2 / Biso min: 8.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→51.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|