+Open data
-Basic information
Entry | Database: PDB / ID: 1iuk | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of native ID.343 from Thermus thermophilus | ||||||
Components | hypothetical protein TT1466Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | CoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CoA-binding domain-containing protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wada, T. / Shirouzu, M. / Park, S.-Y. / Tame, J.R. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of a conserved CoA-binding protein synthesized by a cell-free system. Authors: Wada, T. / Shirouzu, M. / Terada, T. / Ishizuka, Y. / Matsuda, T. / Kigawa, T. / Kuramitsu, S. / Park, S.Y. / Tame, J.R. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iuk.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iuk.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/1iuk ftp://data.pdbj.org/pub/pdb/validation_reports/iu/1iuk | HTTPS FTP |
---|
-Related structure data
Related structure data | 1iulSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15889.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GHJ5 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 35.67 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Details: PEG400, temperature 293K | |||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 4, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 13461 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.122 / % possible all: 80.1 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 24119 / Num. measured all: 62895 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 80.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IUL Resolution: 1.7→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|