[English] 日本語
![](img/lk-miru.gif)
- PDB-3jqj: Crystal structure of the molybdenum cofactor biosynthesis protein... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3jqj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8 | ||||||
![]() | Molybdenum cofactor biosynthesis protein C | ||||||
![]() | BIOSYNTHETIC PROTEIN / MOAC / MOLYBDENUM COFACTOR (MOCO) / MOCO BIOSYNTHESIS / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / Molybdenum cofactor biosynthesis | ||||||
Function / homology | ![]() cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process / GTP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanaujia, S.P. / Jeyakanthan, J. / Nakagawa, N. / Sekar, K. / Baba, S. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8 Authors: Kanaujia, S.P. / Jeyakanthan, J. / Nakagawa, N. / Balasubramaniam, S. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Sekar, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 361.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 294.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 565 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 597.7 KB | Display | |
Data in XML | ![]() | 81.8 KB | Display | |
Data in CIF | ![]() | 110.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jqkC ![]() 3jqmC ![]() 1ekrS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16946.742 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-PGR / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 25%, 1,2-PROPANEDIOL, 5% PEG 3000, 0.1M PHOSPHATE-CITRATE PH 4.2, 10% GLYCEROL,, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 2006 / Details: RH COATED BENT-CYLINDRICAL MIRROR |
Radiation | Monochromator: SI-111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 121501 / % possible obs: 99.9 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.172 / Num. unique all: 12072 / Rsym value: 0.174 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EKR Resolution: 1.9→49.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 604951.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.0318 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.66 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| ||||||||||||||||||||
Xplor file |
|