+Open data
-Basic information
Entry | Database: PDB / ID: 1w4v | ||||||
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Title | structure of the oxidised form of human thioredoxin 2 | ||||||
Components | THIOREDOXIN, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN / ANTIOXIDANT ENZYME / MITOCHONDRION / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Smeets, A. / Evrard, C. / Declercq, J.P. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w4v.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4v.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w4v_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 1w4v_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 1w4v_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1w4v_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4v ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4v | HTTPS FTP |
-Related structure data
Related structure data | 1uvzSC 1w89C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: Q99757 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979909 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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