[English] 日本語
![](img/lk-miru.gif)
- PDB-5xd2: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xd2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and manganese | ||||||
![]() | NUDIX family protein | ||||||
![]() | HYDROLASE / Nudix enzyme / histidine phosphatase domain / intermolecular interface binding / diadenosine polyphosphates / enzyme action / fluoride inhibition | ||||||
Function / homology | ![]() 8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / 8-oxo-dGDP phosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arif, S.M. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() Title: Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1 Authors: Arif, S.M. / Varshney, U. / Vijayan, M. #1: ![]() Title: Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M. #2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2012 Title: Crystallization and preliminary X-ray studies of MutT1 (MSMEG_2390) from Mycobacterium smegmatis. Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xd1C ![]() 5xd3C ![]() 5xd4C ![]() 5xd5C ![]() 5gg5S C: citing same article ( 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: 38153.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2390 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 299 molecules ![](data/chem/img/5FA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-5FA / | ||
---|---|---|---|
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 0.2M sodium acetate trihydrate, 0.1M Tris-HCl pH 8.5, 30%(w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.55 Å / Num. obs: 30580 / % possible obs: 100 % / Redundancy: 4.2 % / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4432 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5gg5 Resolution: 1.75→43.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.166 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.893 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→43.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|