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- PDB-3rtd: Crystal structure of tm0922, a fusion of a domain of unknown func... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rtd | ||||||
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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 NADH and ADP. | ||||||
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![]() | 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 / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209 KB | Display | ![]() |
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PDB format | ![]() | 164.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.1 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 ![]() 3rt9C ![]() 3rtaC ![]() 3rtbC ![]() 3rtcC ![]() 3rteC ![]() 3rtgC ![]() 3ru2C ![]() 3ru3C ![]() 2ax3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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 |
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#2: Protein/peptide | Mass: 806.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unknown peptide, probably from expression host / Source: (natural) ![]() ![]() |
-Non-polymers , 6 types, 75 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NAX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NAX.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-NAI / |
#6: Chemical | ChemComp-ADP / |
#7: Chemical | ChemComp-NAX / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2010 / Details: BERYLLIUM LENSES |
Diffraction measurement | Details: 1.00 degrees, 8.3 sec, detector distance 200.00 mm / Method: \w scans |
Radiation | Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.067 / Number: 152950 |
Reflection | Resolution: 2.3→50 Å / Num. all: 26315 / Num. obs: 25944 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 23.461 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.832 / Rsym value: 0.751 / % possible all: 98 |
Cell measurement | Reflection used: 152950 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AX3 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 10.875 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: 153.77 Å2 / Biso mean: 44.989 Å2 / Biso min: 22.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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