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- PDB-2bja: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bja | ||||||
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Title | Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NADH | ||||||
![]() | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / 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. / Tahirov, T.H. | ||||||
![]() | ![]() Title: Crystal Structure of Thermus Thermophilus Delta1-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 | ![]() | 228.1 KB | Display | ![]() |
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PDB format | ![]() | 182.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 67.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uzbSC ![]() 2bhpC ![]() 2bhqC ![]() 2bjkC ![]() 2iy6C C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.97656, -0.21521, -0.00416), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57129.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OXIDATION OF CYS TO CSO (S-HYDROXYL -CYSTEINE) AT A 322 AND B 322 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 816 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MRD / ( | #6: Chemical | ChemComp-MPD / ( | #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: 50.4 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: PROTEIN WAS CRYSTALLIZED FROM 36% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD,CA.5MM DELTA1-PYRROLINE-5 CARBOXYLATE AND 50 MM SODIUM ACETATE/HCL, PH 5.2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 14, 2004 / Details: MIRRORS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 85247 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.26 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.15 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UZB Resolution: 1.9→37.29 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 397651.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE ARE CISPEPS AT A154-155 AND B154-155.NAHS ARE DISORDERED. MOST PARTS OF DISORDERED REGIONS OF NAHS COULD NOT BE MODELED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.5945 Å2 / ksol: 0.418808 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→37.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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