[English] 日本語
![](img/lk-miru.gif)
- PDB-1j1f: Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1j1f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP | ||||||
![]() | RIBONUCLEASE MC1 | ||||||
![]() | HYDROLASE / Nucleic acid / RNA | ||||||
Function / homology | ![]() ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M. | ||||||
![]() | ![]() Title: Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity Authors: Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M. #1: ![]() Title: Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution Authors: Nakagawa, A. / Tanaka, I. / Sakai, R. / Nakashima, T. / Funatsu, G. / Kimura, M. #2: ![]() Title: Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity Authors: Suzuki, A. / Yao, M. / Tanaka, I. / Numata, T. / Kikukawa, S. / Yamasaki, N. / Kimura, M. #3: ![]() Title: Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity Authors: Numata, T. / Suzuki, A. / Yao, M. / Tanaka, I. / Kimura, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 779.5 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j1gC ![]() 1ucgC ![]() 1bk7S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21344.109 Da / Num. of mol.: 1 / Mutation: N71T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-5GP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M ammonium acetate, 0.1M tri-sodium citrate, 27.5% PEG8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / 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. all: 31008 / Num. obs: 31008 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3 / Num. unique all: 2890 / % possible all: 92.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK7 Resolution: 1.6→19.04 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1703 Å2 / ksol: 0.367496 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|