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Yorodumi- PDB-5g30: Crystallographic structure of mutant D60S of thioredoxin from Lit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g30 | ||||||
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Title | Crystallographic structure of mutant D60S of thioredoxin from Litopenaeus vannamei | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMEI / MUTANT / DISULFIDE BOND | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LITOPENAEUS VANNAMEI (Pacific white shrimp) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Campos-Acevedo, A.A. / Rudino-Pinera, E. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei. Authors: Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Perez, J. / Rudino-Pinera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g30.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g30.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 5g30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g30 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g30 | HTTPS FTP |
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-Related structure data
Related structure data | 5g2zC 5g31C 3zzxS C: citing same article (ref.) 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: 11930.700 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11. Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp) Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: B1PWB9, thioredoxin-disulfide reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENILALAN | |
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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: 2.02 Å3/Da / Density % sol: 39.17 % / Description: NONE |
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Crystal grow | pH: 6 Details: 10 % (W/V) POLYETHYLENE GLYCOL 8,000. 100 MM MES PH 6.0. 200 MM ZINC ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.46 Å / Num. obs: 45126 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZX Resolution: 1.65→19.465 Å / SU ML: 0.18 / σ(F): 1.39 / Phase error: 19.9 / 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: 19.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.465 Å
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Refine LS restraints |
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LS refinement shell |
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