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- PDB-1yxo: Crystal Structure of pyridoxal phosphate biosynthetic protein Pdx... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yxo | ||||||
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Title | Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593 | ||||||
![]() | 4-hydroxythreonine-4-phosphate dehydrogenase 1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Xu, X. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593 Authors: Liu, Y. / Xu, X. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 35247.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9I5U4, ![]() #2: Chemical | #3: Chemical | ChemComp-EOH / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.95 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004 | ||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.01→80 Å / Num. all: 43764 / Num. obs: 42938 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 8.5 | ||||||||||||||||||||
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.05 / Num. unique all: 4188 / Rsym value: 0.201 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: none Resolution: 2.01→36.68 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 410646.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: O v8.0 was used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1599 Å2 / ksol: 0.340458 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→36.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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