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- PDB-3jqm: Binding of 5'-GTP to molybdenum cofactor biosynthesis protein Moa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jqm | ||||||
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Title | Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC 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. / Shinkai, A. / Kuramitsu, S. / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.9 KB | Display | ![]() |
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PDB format | ![]() | 226.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 84.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jqjSC ![]() 3jqkC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 16946.742 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 475 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-FLC / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.23 % |
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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, 10mM 5'-GTP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 23, 2007 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 41061 / % possible obs: 96.1 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.084 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.53 / Num. unique all: 3786 / Rsym value: 0.433 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3JQJ Resolution: 2.5→29.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 445812.55 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.6621 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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