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- PDB-2bhp: 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: 2bhp | ||||||
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Title | Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD. | ||||||
![]() | 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 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 | ![]() | 241.2 KB | Display | ![]() |
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PDB format | ![]() | 193.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 49.5 KB | Display | |
Data in CIF | ![]() | 76.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uzbSC ![]() 2bhqC ![]() 2bjaC ![]() 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9778, -0.20933, -0.00891), 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, 1219 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / #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 % |
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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 5 MM NAD. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 26, 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: 1.8→50 Å / Num. obs: 99097 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 6.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UZB Resolution: 1.8→44.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 703397.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THERE ARE DISORDERD REGIONS IN NADS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 81.3375 Å2 / ksol: 0.432719 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→44.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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