[English] 日本語
Yorodumi- PDB-1tjn: Crystal structure of hypothetical protein af0721 from Archaeoglob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hypothetical protein af0721 from Archaeoglobus fulgidus | ||||||
Components | Sirohydrochlorin cobaltochelatase | ||||||
Keywords | LYASE / af0721 / APC5049 / Midwest Consortium for Structural Genomics / Protein Structure Initiative / A. fulgidus / structural genomics / PSI / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / tetrapyrrole binding / cobalt ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å | ||||||
Authors | Yin, J. / Xu, X.L. / Cuff, M. / Walker, J.R. / Edwards, A. / Savchenko, A. / James, M.N.G. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of af0721: a hypothetical protein bearing sequence similarity with class II chelatases in cobalamin synthesis Authors: Yin, J. / Xu, X.L. / Cuff, M. / Walker, J.R. / Edwards, A. / Savchenko, A. / James, M.N.G. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE RESIDUES IN THE N-TERMINAL FUSION TAG WERE NOT VISIBLE IN THE DENSITY MAPS, NOR WERE ...SEQUENCE THE RESIDUES IN THE N-TERMINAL FUSION TAG WERE NOT VISIBLE IN THE DENSITY MAPS, NOR WERE THE ADDITIONAL GS RESIDUES AT THE C-TERMINUS. THE AUTHORS SUSPECT THAT PRIOR TO CRYSTALIZATION, SOME SORT OF AUTOCLEAVAGE OCCURED AT THE BOUNDARY BETWEEN THE N-TERMINAL TAG AND THE NATIVE STARTING CODON. THEY NOTICED THIS PHENOMENON FOR A NUMBER OF OTHER PROTEINS THEY EXPRESSED IN A FUSION FORM CONTAINING THE TeV CLEAVAGE SITE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tjn.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tjn.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjn ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjn | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17847.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: CBIX, AF0721 / Plasmid: pET15b / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star References: UniProt: O29537, sirohydrochlorin cobaltochelatase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 0.54 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.9 M AMMONIUM SULFATE, 0.1 M HEPES, 4% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979238 / Wavelength: 0.979374,0.979238,0.964108 | ||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 22, 2004 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 10173 / % possible obs: 85.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | Resolution: 2.01→2.04 Å / % possible all: 82.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.01→19.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.202 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.943 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.264 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→19.46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.01→2.062 Å / Total num. of bins used: 20
|