[English] 日本語
![](img/lk-miru.gif)
- PDB-2ce2: CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ce2 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GDP | ||||||
![]() | GTPASE HRAS![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
![]() | ![]() Title: A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction Authors: Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 92.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2cl0C ![]() 2cl6C ![]() 2cl7C ![]() 2clcC ![]() 2cldC ![]() 2evwC ![]() 4q21S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Number of models | 2 | |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | ![]() Mass: 18799.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: YES Source method: isolated from a genetically manipulated source Details: AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / ![]() |
#4: Chemical | ChemComp-XY2 / |
#5: Water | ChemComp-HOH / ![]() |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 39.6 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PROTEIN SOLUTION: 17.22 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM ...Details: PROTEIN SOLUTION: 17.22 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE, 35% PEG 400 MIXTURE OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.99→50 Å / Num. obs: 82821 / % possible obs: 97 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.96 |
Reflection shell | Resolution: 0.99→1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.33 / % possible all: 96.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4Q21 Resolution: 1→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.202 / SU ML: 0.029 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. THE CLOSE CONTACTS WITH WATER MOLECULES ARE CAUSED BY THE TREATMENT OF THE WHOLE PROTEIN CHAIN WITH TWO ALTERNATIVE CONFORMATIONS, BUT ONLY ONE POSITION PER WATER MOLECULE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|