+Open data
-Basic information
Entry | Database: PDB / ID: 2pca | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | Probable diphthine synthase | ||||||
Keywords | TRANSFERASE / Pyrococcus horikoshii OT3 / Methyltransferase / S-adenosyl-L-methionine / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Sugahara, M. / Taketa, M. / Morikawa, Y. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Sugahara, M. / Taketa, M. / Morikawa, Y. / Matsuura, Y. / Kunishima, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pca.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pca.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pca_validation.pdf.gz | 783.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2pca_full_validation.pdf.gz | 788.3 KB | Display | |
Data in XML | 2pca_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 2pca_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/2pca ftp://data.pdbj.org/pub/pdb/validation_reports/pc/2pca | HTTPS FTP |
-Related structure data
Related structure data | 2e8hC 2hr8C 2huqC 2hutC 2huvC 2huxC 2owfC 2owgC 2owkC 2owuC 2owvC 2p2xC 2p5cC 2p5fC 2p6dC 2p6iC 2p6kC 2p6lC 2p9dC 2pb4C 2pb5C 2pb6C 2pcgC 2pchC 2pciC 2pckC 2pcmC 1wngS 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: 29631.404 Da / Num. of mol.: 2 / Mutation: L83M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: dphB / Plasmid: pET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58456, diphthine synthase #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-SAH / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.3 % |
---|---|
Crystal grow | Temperature: 295 K / Method: oil microbatch / pH: 5.5 Details: 3.86M Sodium formate, 0.1M Acetate, pH5.5, oil microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER / Detector: CCD / Date: Nov 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 53695 / Num. obs: 53695 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 30.037 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.097 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5275 / Rsym value: 0.483 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1wng Resolution: 2→29.15 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.017
|