[English] 日本語
Yorodumi- PDB-1jn4: The Crystal Structure of Ribonuclease A in complex with 2'-deoxyu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jn4 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Ribonuclease A in complex with 2'-deoxyuridine 3'-pyrophosphate (P'-5') adenosine | ||||||
Components | Pancreatic Ribonuclease A | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jardine, A.M. / Leonidas, D.D. / Jenkins, J.L. / Park, C. / Raines, R.T. / Acharya, K.R. / Shapiro, R. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Cleavage of 3',5'-Pyrophosphate-Linked Dinucleotides by Ribonuclease A and Angiogenin Authors: Jardine, A.M. / Leonidas, D.D. / Jenkins, J.L. / Park, C. / Raines, R.T. / Acharya, K.R. / Shapiro, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jn4.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jn4.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jn4_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jn4_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1jn4_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1jn4_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/1jn4 ftp://data.pdbj.org/pub/pdb/validation_reports/jn/1jn4 | HTTPS FTP |
-Related structure data
Related structure data | 1afuS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pankreas / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-139 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.91 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 289K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Details: Leonidas, D.D., (1997) Biochemistry, 36, 5578. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 18095 / Num. obs: 18095 / % possible obs: 84.5 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.086 |
Reflection shell | Resolution: 1.8→1.91 Å / Rsym value: 0.262 / % possible all: 80.8 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 41852 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 80.8 % / Rmerge(I) obs: 0.262 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1afu Resolution: 1.8→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|