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- PDB-1mi8: 2.0 Angstrom crystal structure of a DnaB intein from Synechocysti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mi8 | ||||||
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Title | 2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803 | ||||||
![]() | DnaB intein | ||||||
![]() | HYDROLASE / all beta-strands | ||||||
Function / homology | ![]() primosome complex / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / endonuclease activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ding, Y. / Chen, X. / Ferrandon, S. / Xu, M. / Rao, Z. | ||||||
![]() | ![]() Title: Crystal structure of mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing Authors: Ding, Y. / Xu, M.Q. / Ghosh, I. / Chen, X. / Ferrandon, S. / Lesage, G. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.2 KB | Display | ![]() |
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PDB format | ![]() | 27.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427 KB | Display | ![]() |
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Full document | ![]() | 429.9 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.5 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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1 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit |
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Components
#1: Protein | Mass: 17600.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TETHERED DIMER LINKED BY LESSSLQLSPEIEKLSQ / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q55418, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.92 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG4000, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7.5 | ||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 8, 2002 |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 9307 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 75.5 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 97.6 % / Num. measured all: 107903 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 75.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 7.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.21 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |