[English] 日本語
Yorodumi- PDB-2d16: Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d16 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3 | ||||||
Components | hypothetical protein PH1918Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Ta1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Lokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3 Authors: Lokanath, N.K. / Kunishima, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d16.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d16.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d16 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d16 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1vggS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17662.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-CodonPlus (DE3)-RIL / References: UniProt: O59581 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.3 Details: MES-NaOH, PEG 4000, pH 6.3, microbatch, temperature 295.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å |
---|---|
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: Graphite |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 73383 / Num. obs: 73383 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.65→1.71 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VGG Resolution: 1.65→33.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1827339.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7303 Å2 / ksol: 0.344327 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→33.7 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|