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- PDB-1k75: The L-histidinol dehydrogenase (hisD) structure implicates domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k75 | ||||||
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Title | The L-histidinol dehydrogenase (hisD) structure implicates domain swapping and gene duplication. | ||||||
![]() | L-histidinol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / L-histidinol dehydrogenase / homodimer / Rossmann fold / 4 domains / hisD / L-histidine biosynthesis / NAD cofactor / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | ![]() histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / manganese ion binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barbosa, J.A.R.G. / Sivaraman, J. / Li, Y. / Larocque, R. / Matte, A. / Schrag, J. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
![]() | ![]() Title: Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Authors: Barbosa, J.A.R.G. / Sivaraman, J. / Li, Y. / Larocque, R. / Matte, A. / Schrag, J.D. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.5 KB | Display | ![]() |
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Full document | ![]() | 472.2 KB | Display | |
Data in XML | ![]() | 41.7 KB | Display | |
Data in CIF | ![]() | 64.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kaeC ![]() 1kahC ![]() 1karC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological (functional) hisD is the homodimer in the assymetric unit. No symmetry operations are needed. |
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Components
#1: Protein | Mass: 46434.520 Da / Num. of mol.: 2 / Fragment: Se-Met derived dimer Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, glycerol, imidazole/malic acid buffer, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2000 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→40 Å / Num. all: 91930 / Num. obs: 91930 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.4 | ||||||||||||
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3675 / Rsym value: 0.276 / % possible all: 79.7 | ||||||||||||
Reflection | *PLUS Num. obs: 91330 / Num. measured all: 402344 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 79.7 % / Rmerge(I) obs: 0.276 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Rfactor Rfree error: 0.019
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.78 Å / Rfactor Rwork: 0.244 / Rfactor obs: 0.244 |