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- PDB-1jfl: CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jfl | ||||||
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Title | CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA | ||||||
![]() | ASPARTATE RACEMASE | ||||||
![]() | ISOMERASE / ALPHA-BETA STRUCTURE / HOMO-DIMER / HOMOLOGOUS DOMAINS | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, L.J. / Iwata, K. / Kita, A. / Kawarabayasi, Y. / Yohda, M. / Miki, K. | ||||||
![]() | ![]() Title: Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. Authors: Liu, L. / Iwata, K. / Kita, A. / Kawarabayasi, Y. / Yohda, M. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.5 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.8 KB | Display | ![]() |
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Full document | ![]() | 373.1 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 25193.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 4 Details: PEG6000, sodium citrate, calcium chloride, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Details: Liu, L., (2001) Acta Crystallogr., D57, 1674. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. all: 37943 / Num. obs: 37256 / % possible obs: 98.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.055 / Net I/σ(I): 8.9 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5352 / Rsym value: 0.15 / % possible all: 98.4 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 191528 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.2 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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