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- PDB-1lwt: Crystal structure of the intein homing endonuclease PI-SceI bound... -
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Basic information
Entry | Database: PDB / ID: 1lwt | ||||||
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Title | Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA (Ca2+ free) | ||||||
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![]() | HYDROLASE/DNA / HOMING ENDONUCLEASE / PROTEIN-DNA COMPLEX / INTEIN / ENDONUCLEASE / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing / intron homing / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / H+-transporting two-sector ATPase / proton transmembrane transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moure, C.M. / Gimble, F.S. / Quiocho, F.A. | ||||||
![]() | ![]() Title: Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Authors: Moure, C.M. / Gimble, F.S. / Quiocho, F.A. #1: ![]() Title: Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity Authors: Duan, X. / Gimble, F.S. / Quiocho, F.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 | ![]() | 136.3 KB | Display | ![]() |
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PDB format | ![]() | 108.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 487 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lwsSC S: Starting model for refinement C: citing same article ( |
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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: DNA chain | Mass: 11599.467 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 11172.185 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 51379.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VMA1 / Plasmid: PT7PI-SCEI / Production host: ![]() ![]() References: UniProt: P17255, Hydrolases; Acting on ester bonds |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 3550, na citrate, ammonium acetate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 12363 / Num. obs: 12363 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.193 / Num. unique all: 999 / Rsym value: 0.193 / % possible all: 69.8 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 117632 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 69.9 % / Rmerge(I) obs: 0.193 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LWS Resolution: 3.2→24.49 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.18428 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.53 Å / Luzzati sigma a free: 0.59 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→24.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.35 Å / Rfactor Rfree error: 0.4 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor all: 0.248 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.242 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.353 / Rfactor Rwork: 0.301 |