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Open data
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Basic information
Entry | Database: PDB / ID: 1w4v | ||||||
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Title | structure of the oxidised form of human thioredoxin 2 | ||||||
![]() | THIOREDOXIN, MITOCHONDRIAL | ||||||
![]() | OXIDOREDUCTASE / THIOREDOXIN / ANTIOXIDANT ENZYME / MITOCHONDRION / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() peptide-methionine (R)-S-oxide reductase activity / Degradation of cysteine and homocysteine / peptide-methionine (S)-S-oxide reductase activity / Detoxification of Reactive Oxygen Species / cellular response to nutrient levels / protein-disulfide reductase activity / response to axon injury / response to glucose / cell redox homeostasis / response to hormone ...peptide-methionine (R)-S-oxide reductase activity / Degradation of cysteine and homocysteine / peptide-methionine (S)-S-oxide reductase activity / Detoxification of Reactive Oxygen Species / cellular response to nutrient levels / protein-disulfide reductase activity / response to axon injury / response to glucose / cell redox homeostasis / response to hormone / response to organic cyclic compound / response to oxidative stress / response to hypoxia / mitochondrial matrix / response to xenobiotic stimulus / neuronal cell body / dendrite / protein-containing complex binding / nucleolus / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smeets, A. / Evrard, C. / Declercq, J.P. | ||||||
![]() | ![]() Title: Crystal Structures of Oxidized and Reduced Forms of Human Mitochondrial Thioredoxin 2. Authors: Smeets, A. / Evrard, C. / Landtmeters, M. / Marchand, C. / Knoops, B. / Declercq, J.P. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Human Mitochondrial Thioredoxin Authors: Damdimopoulos, A.E. / Miranda-Vizuete, A. / Pelto-Huikkos, M. / Gustafsson, J.A. / Spyrou, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.6 KB | Display | ![]() |
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PDB format | ![]() | 121.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uvzSC ![]() 1w89C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 13288.154 Da / Num. of mol.: 6 / Fragment: RESIDUE 60-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | THIOREDOXI | Sequence details | AMINO ACID NUMBERING STARTS AT THR1 WHICH IS THE FIRST AMINO ACID OF THE PROCESSED PROTEIN WITHOUT ...AMINO ACID NUMBERING STARTS AT THR1 WHICH IS THE FIRST AMINO ACID OF THE PROCESSED PROTEIN WITHOUT ITS MITOCHONDR | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | pH: 4.6 Details: PEG 3350 22% (W/V) NA ACETATE 0.1M (PH 4.6) AMMONIUM SULFATE 0.2M DTT 1MM. SOAKING IN A H2O2 SOLUTION 1MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2003 / Details: M1 AND M2 MIRRORS |
Radiation | Monochromator: FLAT AND N2 COOLED AND SAGITTALY BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979909 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 65984 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.22 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.67 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.45 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UVZ Resolution: 1.8→19.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.158 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.128 / 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: 11.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.32 Å
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Refine LS restraints |
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