+Open data
-Basic information
Entry | Database: PDB / ID: 2wz9 | ||||||
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Title | Crystal structure of the thioredoxin domain of human TXNL2 | ||||||
Components | GLUTAREDOXIN-3 | ||||||
Keywords | PROTEIN BINDING | ||||||
Function / homology | Function and homology information protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / iron-sulfur cluster assembly complex / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / protein kinase C binding / Iron uptake and transport ...protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / iron-sulfur cluster assembly complex / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / protein kinase C binding / Iron uptake and transport / Z disc / cell cortex / intracellular iron ion homeostasis / dendrite / RNA binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Vollmar, M. / Johannson, C. / Cocking, R. / Pike, A.C.W. / Muniz, J.R.C. / Edwards, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Kavanagh, K.L. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Thioredoxin Domain of Human Txnl2 Authors: Vollmar, M. / Johannson, C. / Cocking, R. / Pike, A.C.W. / Muniz, J.R.C. / Edwards, A. / von Delft, F. / Bountra, C. / Kavanagh, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wz9.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wz9.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wz9 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wz9 | HTTPS FTP |
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-Related structure data
Related structure data | 2diyS 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: 16629.838 Da / Num. of mol.: 1 / Fragment: THIOREDOXIN DOMAIN, RESIDUES 2-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O76003 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE TOWARDS C TERMINUS CARRIES SEVEN MUTATIONS INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.49 % / Description: NONE |
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Crystal grow | Details: 1.4 M AMMONIUM CITRATE, PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→34.47 Å / Num. obs: 19534 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DIY Resolution: 1.55→58.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.253 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→58.6 Å
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Refine LS restraints |
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