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- PDB-6a0r: Homoserine dehydrogenase from Thermus thermophilus HB8 unliganded form -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a0r | ||||||
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Title | Homoserine dehydrogenase from Thermus thermophilus HB8 unliganded form | ||||||
![]() | Homoserine dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / nad-dependent / dehydrogenase | ||||||
Function / homology | ![]() homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Akai, S. / Ikushiro, H. / Sawai, T. / Yano, T. / Kamiya, N. / Miyahara, I. | ||||||
![]() | ![]() Title: The crystal structure of homoserine dehydrogenase complexed with l-homoserine and NADPH in a closed form Authors: Akai, S. / Ikushiro, H. / Sawai, T. / Yano, T. / Kamiya, N. / Miyahara, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.3 KB | Display | ![]() |
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PDB format | ![]() | 130.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6a0sC ![]() 6a0tC ![]() 6a0uC ![]() 5xdfS 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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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 35529.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 783 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-UNL / | Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | Authors state that they do not use 4-~{tert}-butylbenzoic acid or the derivatives as a ...Authors state that they do not use 4-~{tert}-butylbenzoic acid or the derivatives as a crystallization solution. Therefore, even though the electron density map is clearly 4-~{tert}-butylbenzoic acid, the ligand is assigned to 'unknown ligand (UNL)' |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium formate, CAPS pH 10.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. obs: 104929 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 48.7 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XDF Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / 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: 28.115 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→20 Å
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Refine LS restraints |
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