+Open data
-Basic information
Entry | Database: PDB / ID: 1tj6 | ||||||
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Title | Crystal structure of the Xenopus tropicalis Spred1 EVH-1 domain | ||||||
Components | Spred1 | ||||||
Keywords | SIGNALING PROTEIN / EVH-1 / Spred | ||||||
Function / homology | Function and homology information FGFRL1 modulation of FGFR1 signaling / negative regulation of MAPK cascade / phosphatase binding / protein kinase binding / plasma membrane Similarity search - Function | ||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Harmer, N.J. / Sivak, J. / Amaya, E. / Blundell, T.L. | ||||||
Citation | Journal: To be Published Title: 1.65A Crystal structure of the X. tropicalis Spred1 Enabled/Vasodilator-stimulated phosphoprotein homology-1 domain Authors: Harmer, N.J. / Sivak, J. / Amaya, E. / Blundell, T.L. | ||||||
History |
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Remark 999 | SEQUENCE AT THE TIME OF DEPOSITION, THE SEQUENCE OF THE PROTEIN HAD NOT YET BEEN DEPOSITED IN ANY ...SEQUENCE AT THE TIME OF DEPOSITION, THE SEQUENCE OF THE PROTEIN HAD NOT YET BEEN DEPOSITED IN ANY REFERENCE SEQUENCE DATABASE. RESIDUE 68 WAS MUTATED FROM VAL TO ILE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tj6.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tj6.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tj6_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 1tj6_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 1tj6_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1tj6_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tj6 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tj6 | HTTPS FTP |
-Related structure data
Related structure data | 1evhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12984.564 Da / Num. of mol.: 2 / Fragment: EVH-1 domain / Mutation: V68I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: Spred1 / Plasmid: pETG-10a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 BL21 (DE3) / References: UniProt: Q66JG9 #2: 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: 1.94 Å3/Da / Density % sol: 36.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, potassium fluoride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 2004 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25 Å / Num. all: 24189 / Num. obs: 23273 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 9.35 / Num. unique all: 1497 / Rsym value: 0.211 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EVH Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 1.116 / SU ML: 0.04 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.099 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
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