[English] 日本語
![](img/lk-miru.gif)
- PDB-1afk: CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1afk | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE-3'-PHOSPHATE | ||||||
![]() | RIBONUCLEASE A | ||||||
![]() | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leonidas, D.D. / Acharya, K.R. | ||||||
![]() | ![]() Title: Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution. Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1aflC ![]() 1afuC ![]() 3rn3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.59498, -0.803215, 0.029055), Vector: |
-
Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 20 MM SODIUM CITRATE, PH 5.5 AND THEN SOAKED WITH 1MM 5' DIPHOSPHOADENOSINE 3'-PHOSPHATE FOR 2.5 HRS AT 16 C, temperature 289K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 24687 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.7→1.77 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.339 / % possible all: 82.4 |
Reflection | *PLUS Num. measured all: 73892 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RN3 Resolution: 1.7→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|