[English] 日本語
![](img/lk-miru.gif)
- PDB-3rt9: Crystal structure of tm0922, a fusion of a domain of unknown func... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3rt9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Coenzyme A | ||||||
![]() |
| ||||||
![]() | LYASE / Unknown function / ADP/ATP-dependent NAD(P)H-hydrate dehydratase | ||||||
Function / homology | ![]() NAD(P)H-hydrate epimerase / metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ATP-dependent NAD(P)H-hydrate dehydratase activity / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shumilin, I.A. / Cymborowski, M. / Lesley, S.A. / Minor, W. | ||||||
![]() | ![]() Title: Identification of unknown protein function using metabolite cocktail screening. Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 208.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rnoC ![]() 3ro7C ![]() 3roeC ![]() 3rogC ![]() 3roxC ![]() 3rozC ![]() 3rphC ![]() 3rpzC ![]() 3rq2C ![]() 3rq5C ![]() 3rq6C ![]() 3rq8C ![]() 3rqhC ![]() 3rqqC ![]() 3rqxC ![]() 3rrbC ![]() 3rreC ![]() 3rrfC ![]() 3rrjC ![]() 3rs8C ![]() 3rs9C ![]() 3rsfC ![]() 3rsgC ![]() 3rsqC ![]() 3rssC ![]() 3rt7C ![]() 3rtaC ![]() 3rtbC ![]() 3rtcC ![]() 3rtdC ![]() 3rteC ![]() 3rtgC ![]() 3ru2C ![]() 3ru3C ![]() 2ax3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 8||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54527.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X024, ATP-dependent NAD(P)H-hydrate dehydratase | ||
---|---|---|---|
#2: Protein/peptide | Mass: 735.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unknown peptide, probably from expression host / Source: (natural) ![]() ![]() | ||
#3: Chemical | ChemComp-K / | ||
#4: Chemical | ChemComp-COA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2009 / Details: MIRRORS |
Diffraction measurement | Details: 1.00 degrees, 15.00 sec, detector distance 180.00 mm |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.069 / Number: 337661 |
Reflection | Resolution: 1.95→50 Å / Num. all: 42893 / Num. obs: 42640 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 31.75 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.247 / Rsym value: 0.848 / % possible all: 98.7 |
Cell measurement | Reflection used: 337661 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AX3 Resolution: 1.952→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.475 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.06 Å2 / Biso mean: 35.091 Å2 / Biso min: 18.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.952→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.952→2.003 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|