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Yorodumi- PDB-2wul: CRYSTAL STRUCTURE OF THE HUMAN GLUTAREDOXIN 5 WITH BOUND GLUTATHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wul | |||||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN GLUTAREDOXIN 5 WITH BOUND GLUTATHIONE IN AN FES CLUSTER | |||||||||
Components | GLUTAREDOXIN RELATED PROTEIN 5 | |||||||||
Keywords | OXIDOREDUCTASE / CHROMOSOME 14 OPEN READING FRAME 87 / THIOREDOXIN FAMILY / GLRX5 / PR01238 / FLB4739 | |||||||||
Function / homology | Function and homology information protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis ...protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / mitochondrial matrix / neuronal cell body / dendrite / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||
Authors | Roos, A.K. / Johansson, C. / Guo, K. / Yue, W.W. / Pike, A.C.W. / Cooper, C.D.O. / Pilka, E.S. / Kavanagh, K.L. / Chaikuad, A. / von Delft, F. ...Roos, A.K. / Johansson, C. / Guo, K. / Yue, W.W. / Pike, A.C.W. / Cooper, C.D.O. / Pilka, E.S. / Kavanagh, K.L. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | |||||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: The Crystal Structure of Human Glrx5: Iron Sulphur Cluster Coordination, Tetrameric Assembly and Monomer Activity. Authors: Johansson, C. / Roos, A.K. / Montano, S.J. / Sengupta, R. / Filippakopoulos, P. / Guo, K. / von Delft, F. / Holmgren, A. / Oppermann, U. / 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 | 2wul.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wul.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wul_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2wul_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2wul_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2wul_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/2wul ftp://data.pdbj.org/pub/pdb/validation_reports/wu/2wul | HTTPS FTP |
-Related structure data
Related structure data | 2e7pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 12865.564 Da / Num. of mol.: 4 / Fragment: RESIDUES 35-150 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: Q86SX6 |
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-Non-polymers , 5 types, 104 molecules
#2: Chemical | ChemComp-GSH / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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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: 2.66 Å3/Da / Density % sol: 53.8 % Description: INITIAL PHASES BY SE-SAD ALLOWED AN INITIAL MODEL BASED ON 2E7P TO BE PLACED FOR SUBSEQUENT MR INTO THE HIGHER RESOLUTION DATA |
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Crystal grow | pH: 6.5 Details: 50% PEG300, 0.2 M MGCL2, 0.1 M CACODYLATE PH 6.5, 0.01 M SPERMINE TETRAHYDROCHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979, 0.9794 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→69.05 Å / Num. obs: 22752 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.2 | |||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 2E7P Resolution: 2.4→66.07 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.349 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.087 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→66.07 Å
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Refine LS restraints |
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