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Yorodumi- PDB-4v2m: Crystallographic structure of thioredoxin from Litopenaeus vannam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v2m | ||||||
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Title | Crystallographic structure of thioredoxin from Litopenaeus vannamei: Radiation damage effect at 34 MGy, focused in disulfide bonds. | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMIE / RADIATION DAMAGE / DISULFIDE BOND | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LITOPENAEUS VANNAMEI (Pacific white shrimp) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 Å | ||||||
Authors | Campos-Acevedo, A.A. / Rudino-Pinera, E. | ||||||
Citation | Journal: Molecules / Year: 2014 Title: Crystallographic Studies Evidencing the High Energy Tolerance to Disrupting the Interface Disulfide Bond of Thioredoxin 1 from White Leg Shrimp Litopenaeus Vannamei. Authors: Campos-Acevedo, A.A. / 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 | 4v2m.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2m.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v2m_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 4v2m_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 4v2m_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4v2m_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2m ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2m | HTTPS FTP |
-Related structure data
Related structure data | 4v2lC 4v2nC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11958.710 Da / Num. of mol.: 2 / 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 | ChemComp-GOL / | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Sequence details | A SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENYLALAN | |
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 2.0 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→27.8 Å / Num. obs: 18958 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 30.01 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.84→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZX Resolution: 1.841→27.802 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.34 / 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: 39.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.841→27.802 Å
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Refine LS restraints |
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LS refinement shell |
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