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Yorodumi- PDB-1p8k: The structure and DNA recognition of a bifunctional homing endonu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p8k | ||||||
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Title | The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information intron homing / RNA splicing / mRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Stoddard, B.L. / Bolduc, J.M. | ||||||
Citation | Journal: Genes Dev. / Year: 2003 Title: Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Authors: Bolduc, J.M. / Spiegel, P.C. / Chatterjee, P. / Brady, K.L. / Downing, M.E. / Caprara, M.G. / Waring, R.B. / Stoddard, B.L. | ||||||
History |
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Remark 999 | SEQUENCE The author claims that Arg61 is correct. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p8k.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8k.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1p8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p8k_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 1p8k_full_validation.pdf.gz | 483.6 KB | Display | |
Data in XML | 1p8k_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1p8k_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8k ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8k | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 4 types, 4 molecules ABCD
#1: DNA chain | Mass: 5588.601 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4931.230 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: DNA chain | Mass: 4481.899 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein / Non-polymers , 2 types, 3 molecules Z
#5: Protein | Mass: 29615.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Gene: Aspergillus nidulans / Production host: Escherichia coli (E. coli) References: UniProt: P03880, Hydrolases; Acting on ester bonds |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG3350, KCl, MgCl2, sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2002 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.21 / % possible all: 61.8 |
Reflection | *PLUS Num. obs: 16749 / Redundancy: 12.7 % / Num. measured all: 58621 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 66.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03
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Refinement | *PLUS Rfactor Rfree: 0.262 / Rfactor Rwork: 0.238 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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