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- PDB-4c1a: Coiled coil domain of the ZfL2-1 ORF1 protein from the zebrafish ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c1a | ||||||
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Title | Coiled coil domain of the ZfL2-1 ORF1 protein from the zebrafish ZfL2- 1 retrotransposon | ||||||
![]() | ORF1-ENCODED PROTEIN | ||||||
![]() | HYDROLASE / RETROTRANSPOSITION / RNA-BINDING / MEMBRANE-BINDING / LIPID-BINDING / SELF-ASSOCIATION | ||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / ORF1-encoded protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schneider, A.M. / Weichenrieder, O. | ||||||
![]() | ![]() Title: Structure and Properties of the Esterase from Non-Ltr Retrotransposons Suggest a Role for Lipids in Retrotransposition. Authors: Schneider, A.M. / Schmidt, S. / Jonas, S. / Vollmer, B. / Khazina, E. / Weichenrieder, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c1bC ![]() 1a92S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 4135.833 Da / Num. of mol.: 4 / Fragment: COILED COIL DOMAIN, RESIDUES 15-47 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Sequence details | THE THREE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. THE SAMPLE WAS PROTEOLYZED PRIOR TO ...THE THREE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 200MM NA-THIOCYANATE, 20% PEG 3350, PH=7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97138 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→37 Å / Num. obs: 17462 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.47 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A92 Resolution: 1.55→36.583 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 26.14 / Stereochemistry target values: ML / Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→36.583 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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