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- PDB-3cm0: Crystal structure of adenylate kinase from Thermus thermophilus HB8 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cm0 | ||||||
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Title | Crystal structure of adenylate kinase from Thermus thermophilus HB8 | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / Adenylate kinase / ATP-binding / Cytoplasm / Nucleotide biosynthesis / Nucleotide-binding / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() adenylate kinase / adenylate kinase activity / AMP salvage / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakagawa, N. / Kondo, N. / Masui, R. / Matsuda, Z. / Iwamoto, I. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of adenylate kinase from Thermus thermophilus HB8 Authors: Nakagawa, N. / Kondo, N. / Masui, R. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.2 KB | Display | ![]() |
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PDB format | ![]() | 34.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 418.5 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ak2S S: Starting model for refinement |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20783.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 40% 1,2-propanediol, 0.1M NaAcetate, pH4.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 10, 2003 |
Radiation | Monochromator: Diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 19365 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.243 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AK2 Resolution: 1.8→44.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1140508.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.002 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→44.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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