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Yorodumi- PDB-5c2m: The de novo evolutionary emergence of a symmetrical protein is sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c2m | ||||||
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Title | The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints | ||||||
Components | Predicted protein | ||||||
Keywords | STRUCTURAL PROTEIN / beta-propeller | ||||||
Function / homology | Tachylectin 2 / Tachylectin 2 / Tachylectin 2 superfamily / Tachylectin / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta / Tachylectin 2 domain-containing protein Function and homology information | ||||||
Biological species | Nematostella vectensis (starlet sea anemone) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Smock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S. | ||||||
Citation | Journal: Cell / Year: 2016 Title: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Authors: Smock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c2m.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c2m.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 5c2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/5c2m ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c2m | HTTPS FTP |
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-Related structure data
Related structure data | 5c2nC 1tl2S S: Starting model for refinement 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
#1: Protein | Mass: 28179.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nematostella vectensis (starlet sea anemone) Gene: v1g114158 / Production host: Escherichia coli (E. coli) / References: UniProt: A7SDD2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 292 K / Method: microbatch Details: 0.1M NaF, 0.05 M Bis-Tris propane pH 7.5, 10% polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 19656 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.042 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TL2 Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.783 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.718 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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