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- PDB-2bjk: 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: 2bjk | ||||||
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Title | Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD and citrate. | ||||||
![]() | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / DEHYROGENASE | ||||||
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 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 | ![]() | 245.8 KB | Display | ![]() |
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PDB format | ![]() | 197.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1uzbSC ![]() 2bhpC ![]() 2bhqC ![]() 2bjaC ![]() 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: (0.97687, -0.21369, -0.00718), 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, 1376 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MRD / ( #5: Chemical | ChemComp-MPD / ( #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: 50.1 % |
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Crystal grow | pH: 5.2 Details: PROTEIN WAS CRYSTALLIZED FROM 32% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD AND 10MM MGCL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS-V / Detector: IMAGE PLATE / Date: Oct 22, 2002 / Details: MIRRORS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 511404 / % possible obs: 97.6 % / Observed criterion σ(I): -0.5 / Redundancy: 2.5 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.04→1.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.7 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UZB Resolution: 1.4→33.29 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1404023.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5273 Å2 / ksol: 0.32476 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→33.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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