[English] 日本語
Yorodumi- PDB-1ssd: Understanding protein lids: Structural analysis of active hinge m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ssd | ||||||
---|---|---|---|---|---|---|---|
Title | Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / archae / evolution / flexible loop-6 / TIM / N-hinge | ||||||
Function / homology | Function and homology information Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2004 Title: Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase Authors: Kursula, I. / Salin, M. / Sun, J. / Norledge, B.V. / Haapalainen, A.M. / Sampson, N.S. / Wierenga, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ssd.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ssd.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ssd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/1ssd ftp://data.pdbj.org/pub/pdb/validation_reports/ss/1ssd | HTTPS FTP |
---|
-Related structure data
Related structure data | 1spqC 1sq7C 1ssgC 1su5C 1sw0C 1sw3C 1sw7C 8timS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | asymmetric unit containsa one biological unit, dimer (chains A and B) |
-Components
#1: Protein | Mass: 26588.312 Da / Num. of mol.: 2 / Mutation: K174Y, T175S, A176L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TPI1 / Plasmid: pBSX1c / Production host: Escherichia coli (E. coli) / Strain (production host): DF502 / References: UniProt: P00940, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: citrate, ammonium sulphate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2003 / Details: Bent mirror |
Radiation | Monochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.73 Å / Num. all: 20463 / Num. obs: 20217 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.41 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.095 / Net I/σ(I): 15.1 |
Reflection shell | Highest resolution: 2.9 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2007 / Rsym value: 0.355 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8TIM Resolution: 2.9→19.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.134 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.34 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|