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Yorodumi- PDB-4zbd: Crystal structure of the glutathione transferase URE2P6 from Phan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zbd | ||||||
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Title | Crystal structure of the glutathione transferase URE2P6 from Phanerochaete chrysosporium in complex with glutathione reduced by X-ray irradiation at 100K | ||||||
Components | PcUre2p6 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD / OXYDIZED GLUTATHIONE | ||||||
Function / homology | Function and homology information Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Roret, T. / Didierjean, C. | ||||||
Citation | Journal: Fungal Genet. Biol. / Year: 2015 Title: Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungi. Authors: Roret, T. / Thuillier, A. / Favier, F. / Gelhaye, E. / Didierjean, C. / Morel-Rouhier, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zbd.cif.gz | 297 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zbd.ent.gz | 245.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbd ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbd | HTTPS FTP |
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-Related structure data
Related structure data | 4f0cC 4zb6C 4zb7C 4zb8SC 4zb9C 4zbaC 4zbbC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25567.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4I981*PLUS #2: Chemical | ChemComp-GSH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 278 K / Method: microbatch / Details: 30 % PEG4000, 10mM TRIS pH8.5, 0.2M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→48.3 Å / Num. obs: 198807 / % possible obs: 95.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.073 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.16 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZB8 Resolution: 1.12→26.646 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.73 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→26.646 Å
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Refine LS restraints |
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LS refinement shell |
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