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- PDB-2iy6: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iy6 | ||||||
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Title | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE | ||||||
![]() | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / CITRATE / DEHYROGENASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / cytoplasmic side of plasma membrane / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Inagaki, E. / Sakamoto, K. / Nishio, M. / Yokoyama, S. | ||||||
![]() | ![]() Title: Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase. Authors: Inagaki, E. / Ohshima, N. / Takahashi, H. / Kuroishi, C. / Yokoyama, S. / Tahirov, T.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.3 KB | Display | ![]() |
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PDB format | ![]() | 191 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463 KB | Display | ![]() |
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Full document | ![]() | 355.2 KB | Display | |
Data in XML | ![]() | 47.8 KB | Display | |
Data in CIF | ![]() | 74.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uzbSC ![]() 2bhpC ![]() 2bhqC ![]() 2bjaC ![]() 2bjkC C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.977, -0.215, -0.006), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57113.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1176 molecules ![](data/chem/img/FLC.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 5.2 / Details: 40% MPD, 50MM SODIUM CITRATE PH 5.2. |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 6, 2006 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 100192 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 14 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UZB Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.77 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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