[English] 日本語
Yorodumi- PDB-1gmr: COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gmr | ||||||
---|---|---|---|---|---|---|---|
Title | COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION | ||||||
Components | RIBONUCLEASE SARibonuclease T1 | ||||||
Keywords | HYDROLASE(GUANYLORIBONUCLEASE) | ||||||
Function / homology | Function and homology information ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.77 Å | ||||||
Authors | Sevcik, J. / Hill, C. / Dauter, Z. / Wilson, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution. Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1991 Title: Continuation of the Rnase Sa Work After 1Sar and 2Sar Structures Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gmr.cif.gz | 56 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gmr.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gmr ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gmr | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO A 27 AND PRO B 27 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 10584.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / References: UniProt: P05798, EC: 3.1.27.3 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THERE TOO MANY WATER MOLECULES AT BONDING DISTANCE FROM ATOMS OF 2GP B. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion / Details: referred to Acta Cryst.B47.240-253 1991 | ||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.77 Å / Num. obs: 19476 / % possible obs: 96.3 % / Num. measured all: 56410 / Rmerge(I) obs: 0.042 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.77→10 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.77 Å / Lowest resolution: 10 Å / Num. reflection obs: 19319 / Rfactor obs: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|