[English] 日本語
Yorodumi- PDB-1od6: The Crystal Structure of Phosphopantetheine adenylyltransferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1od6 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Phosphopantetheine adenylyltransferase from Thermus Thermophilus in complex with 4'-phosphopantetheine | ||||||
Components | PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / COENZYME A BIOSYNTHESIS / NUCLEOTIDYLTRANSFERASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Takahashi, H. / Inagaki, E. / Miyano, M. / Tahirov, T.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure and Implications for the Thermal Stability of Phosphopantetheine Adenylyltransferase from Thermus Thermophilus. Authors: Takahashi, H. / Inagaki, E. / Fujimoto, Y. / Kuroishi, C. / Nodake, Y. / Nakamura, Y. / Arisaka, F. / Yutani, K. / Kuramitsu, S. / Yokoyama, S. / Yamamoto, M. / Miyano, M. / Tahirov, T.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1od6.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1od6.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1od6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/1od6 ftp://data.pdbj.org/pub/pdb/validation_reports/od/1od6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1qjcS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17730.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET 11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5SJS9, pantetheine-phosphate adenylyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-PNS / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.3 Details: PROTEIN WAS CRYSTALLIZED FROM 1.1M LISULF, 100 MM MES, PH 6.25. | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 47654 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 8 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. measured all: 334505 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 98.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJC Resolution: 1.5→37.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1745265.87 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.2005 / Rfactor Rwork: 0.1962 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|