+Open data
-Basic information
Entry | Database: PDB / ID: 4e0z | ||||||
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Title | Protelomerase tela R205A covalently complexed with substrate DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / PROTELEMORASE / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information Helix Hairpins - #1780 / Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Shi, K. / Aihara, H. | ||||||
Citation | Journal: Plos Biol. / Year: 2013 Title: An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. Authors: Shi, K. / Huang, W.M. / Aihara, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e0z.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e0z.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e0z_validation.pdf.gz | 853.8 KB | Display | wwPDB validaton report |
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Full document | 4e0z_full_validation.pdf.gz | 862 KB | Display | |
Data in XML | 4e0z_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 4e0z_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/4e0z ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0z | HTTPS FTP |
-Related structure data
Related structure data | 4dwpC 4e0gC 4e0jC 4e0pC 4e0yC 4e10C C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52562.055 Da / Num. of mol.: 1 / Mutation: R205A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: telA, Atu2523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CWV1 |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 3951.639 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 5839.804 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 261 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-DT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. all: 25104 / Num. obs: 25104 / % possible obs: 73.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→35.689 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 29.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.42→35.689 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.7701 Å / Origin y: -11.232 Å / Origin z: 3.2541 Å
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Refinement TLS group | Selection details: all |