[English] 日本語
![](img/lk-miru.gif)
- PDB-4c0k: Crystal structure of Drosophila Miro EF hand and cGTPase domains ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4c0k | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Drosophila Miro EF hand and cGTPase domains bound to one calcium ion (Ca-MiroS) | |||||||||
![]() | MITOCHONDRIAL RHO GTPASE | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() establishment of mitochondrion localization, microtubule-mediated / RHOT2 GTPase cycle / RHOT1 GTPase cycle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Klosowiak, J.L. / Focia, P.J. / Wawrzak, Z. / Chakravarthy, S. / Landahl, E.C. / Freymann, D.M. / Rice, S.E. | |||||||||
![]() | ![]() Title: Structural Coupling of the EF Hand and C-Terminal Gtpase Domains in the Mitochondrial Protein Miro. Authors: Klosowiak, J.L. / Focia, P.J. / Chakravarthy, S. / Landahl, E.C. / Freymann, D.M. / Rice, S.E. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49118.531 Da / Num. of mol.: 1 / Fragment: ELM1, ELM2, AND CGTPASE, RESIDUES 201-617 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Description: DROSOPHILA GENOMICS RESOURCE CENTER CLONE RE22983 Production host: ![]() ![]() ![]() References: UniProt: Q8IMX7, ![]() |
---|
-Non-polymers , 6 types, 77 molecules ![](data/chem/img/HSE.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HSE / ![]() | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-UNX / | ||||||
#4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | ![]() |
-Details
Nonpolymer details | UNKNOWN ATOM OR ION (UNX): UNIDENTIFI |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % Description: MOLECULAR REPLACEMENT MODEL WAS A MIRO STRUCTURE DETERMINED BY SAD PHASING OF SE-MET LABELED PROTEIN. |
---|---|
Crystal grow![]() | pH: 7.4 Details: 5.0MG/ML MIROS, 1.7 M LISO4, 0.1 M BIS-TRIS PH 7.4, 5 MM EGTA; CRYSTAL SOAKED IN 10MM CACL2 FOR 72H PRIOR TO DATA COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→42.1 Å / Num. obs: 15693 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 67.65 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: INITIAL MODEL FROM PRIOR DATASET Resolution: 2.801→42.075 Å / SU ML: 0.39 / σ(F): 1.91 / Phase error: 26.98 / Stereochemistry target values: ML Details: REFINEMENT NUMBER OF REFLECTIONS TREATS ANOMALOUS PAIRS SEPARATELY. A LARGE LOOP COMPRISING RESIDUES 434-441 IS POORLY ORDERED, DESPITE THE SIDECHAINS OF I435 AND L437 CONTRIBUTING TO A ...Details: REFINEMENT NUMBER OF REFLECTIONS TREATS ANOMALOUS PAIRS SEPARATELY. A LARGE LOOP COMPRISING RESIDUES 434-441 IS POORLY ORDERED, DESPITE THE SIDECHAINS OF I435 AND L437 CONTRIBUTING TO A HYDROPHOBIC CRYSTAL CONTACT, AND A SECOND LOOP COMPRISING RESIDUES 561-566 IS ALSO POORLY ORDERED. RESIDUES OF BOTH HAVE BEEN BUILT AS ALA OR GLY WHERE SIDECHAIN POSITIONS COULD NOT BE DETERMINED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→42.075 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|