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Yorodumi- PDB-4hpz: Crystal structure of a TALE protein reveals an extended N-termina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hpz | ||||||
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Title | Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region | ||||||
Components | dTale2 | ||||||
Keywords | DNA BINDING PROTEIN / N-TERMINAL DOMAIN / TAL EFFECTOR | ||||||
Function / homology | TAL effector repeat / TAL effector repeat / dTale2 Function and homology information | ||||||
Biological species | Xanthomonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å | ||||||
Authors | Chai, J. / Han, Z. / Gao, H. | ||||||
Citation | Journal: Cell Res. / Year: 2012 Title: Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region Authors: Gao, H. / Wu, X. / Chai, J. / Han, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hpz.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hpz.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hpz_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 4hpz_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 4hpz_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4hpz_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/4hpz ftp://data.pdbj.org/pub/pdb/validation_reports/hp/4hpz | HTTPS FTP |
-Related structure data
Related structure data | 3v6pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48280.113 Da / Num. of mol.: 1 / Fragment: dTale2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas (bacteria) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7MTL1*PLUS | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS HIGHLY-CONSERVED ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS HIGHLY-CONSERVED PROTEIN WAS CONSTRUCTE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05M MgSO4, 0.05M HEPES, 1.6M Li2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. all: 29024 / Num. obs: 29024 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2.2→2.24 Å / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V6P Resolution: 2.202→14.975 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 26.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.732 Å2 / ksol: 0.392 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.202→14.975 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 17.7169 Å / Origin y: 55.0361 Å / Origin z: -25.2695 Å
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Refinement TLS group | Selection details: all |