+
Open data
-
Basic information
Entry | Database: PDB / ID: 1sd0 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of arginine kinase C271A mutant | ||||||
![]() | Arginine kinase![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gattis, J.L. / Ruben, E. / Fenley, M.O. / Ellington, W.R. / Chapman, M.S. | ||||||
![]() | ![]() Title: The active site cysteine of arginine kinase: structural and functional analysis of partially active mutants Authors: Gattis, J.L. / Ruben, E. / Fenley, M.O. / Ellington, W.R. / Chapman, M.S. #1: ![]() Title: Transition state structure of arginine kinase: Implications for catalysis of bimolecular reactions Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Parthasarathy, G. / Ellington, W.R. / Chapman, M.S. #2: ![]() Title: Refinement of the arginine kianse transition-state analogue complex at 1.2 A resolution: mechanistic insights Authors: Yousef, M.S. / Fabiola, F. / Gattis, J.L. / Somasundaram, T. / Chapman, M.S. #3: ![]() Title: Induced fit in guanidino kinases- comparison of substrate-free and transition state analog structures of arginine kinase Authors: Yousef, M.S. / Clark, S.A. / Pruett, P.K. / Somasundaram, T. / Ellington, W.R. / Chapman, M.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1m15S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 40245.711 Da / Num. of mol.: 1 / Mutation: C271A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ak / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 293 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NO3 / ![]() |
---|---|
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CL / ![]() |
#5: Chemical | ChemComp-ARG / ![]() |
#6: Chemical | ChemComp-ADP / ![]() |
#7: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.31 % |
---|---|
Crystal grow![]() | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, magnesium chloride, HEPES, L-arginine, ADP, sodium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2001 / Details: mirrors |
Radiation | Monochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.27→100 Å / Num. all: 15669 / Num. obs: 15669 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1747 / Rsym value: 0.192 / % possible all: 98.9 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 1m15 Resolution: 2.3→10 Å / Isotropic thermal model: isotropic / Cross valid method: random / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 44 Å2 | ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.38 Å
| ||||||||||||||||||||
Xplor file |
|