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Yorodumi- PDB-4ulx: Crystal structure of ancestral thioredoxin, relative to the last ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ulx | ||||||
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Title | Crystal structure of ancestral thioredoxin, relative to the last common ancestor of the Cyanobacterial, Deinococcus and Thermus groups, LPBCA-L89K mutant. | ||||||
Components | LPBCA-L89K THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / ANCESTRAL | ||||||
Function / homology | Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Gavira, J.A. / Risso, V.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
Citation | Journal: Mol.Biol.Evol. / Year: 2015 Title: Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences Throughout Evolutionary History. Authors: Risso, V.A. / Manssour-Triedo, F. / Delgado-Delgado, A. / Arco, R. / Barroso-Deljesus, A. / Ingles-Prieto, A. / Godoy-Ruiz, R. / Gavira, J.A. / Gaucher, E.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ulx.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ulx.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ulx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ulx_validation.pdf.gz | 418.9 KB | Display | wwPDB validaton report |
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Full document | 4ulx_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 4ulx_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 4ulx_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/4ulx ftp://data.pdbj.org/pub/pdb/validation_reports/ul/4ulx | HTTPS FTP |
-Related structure data
Related structure data | 2yj7S 4d27 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
#1: Protein | Mass: 12021.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: EC: 4.7.1.4 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 4 Details: COUNTERDIFFUSION METHOD: 0.1M NA ACETATE PH 4.0, 20% PEG 400, 15% PEG 4000 & 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→32.79 Å / Num. obs: 3761 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 29.79 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.06 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YJ7 Resolution: 2.35→32.794 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 28.36 / 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 | Biso mean: 36.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→32.794 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3503→32.7971 Å
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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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