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- PDB-2j40: 1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j40 | ||||||
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Title | 1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD. | ||||||
![]() | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / GLUTAMATE / TYPE II HYPERPROLINMIA / 1-PYRROLINE-5-CARBOXYLATE / PROLINE METHABOLIC PATHWAY | ||||||
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 Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer Authors: Inagaki, E. / Sakamoto, K. / Nishio, M. / 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 | ![]() | 230.2 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j5nC ![]() 2bjkS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.977, -0.215, -0.004), 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: C 322 IS OXIDATED TO BE S-HYDROXYCYSTEINE / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 804 molecules ![](data/chem/img/PRO.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MPD / ( #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | Q5SI02_THET8 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: PROTEIN WAS CRYSTALLIZED FROM 37.5% MRD, 50 MM SODIUM CITRATE, PH 5.2; THEN SOAKED IN 2MM NAD, 100MM L-PROLINE, 50 MM SODIUM ACETATE PH5.2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: May 24, 2006 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 62989 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BJK Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.868 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.157 / 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: 19.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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