+Open data
-Basic information
Entry | Database: PDB / ID: 1oc8 | ||||||
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Title | TRYPAREDOXIN II FROM C.FASCICULATA SOLVED BY MR | ||||||
Components | TRYPAREDOXIN II | ||||||
Keywords | ELECTRON TRANSPORT / TRYPAREDOXIN II | ||||||
Function / homology | Function and homology information protein-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity Similarity search - Function | ||||||
Biological species | CRITHIDIA FASCICULATA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Leonard, G.A. / Micossi, E. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Tryparedoxins from Crithidia Fasciculata and Trypanosoma Brucei: Photoreduction of the Redox Disulfide Using Synchrotron Radiation and Evidence for a Conformational Switch Implicated in Function Authors: Alphey, M.S. / Gabrielsen, M. / Micossi, E. / Leonard, G.A. / Mcsweeney, S.M. / Ravelli, R.B.G. / Tetaud, E. / Fairlamb, A.H. / Bond, C.S. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oc8.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oc8.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 1oc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1oc8 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1oc8 | HTTPS FTP |
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-Related structure data
Related structure data | 1o73C 1o7uC 1o85C 1o8wC 1o8xC 1oc9C 1qk8S C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17163.721 Da / Num. of mol.: 2 / Fragment: RESIDUES 14-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: O77093 #2: Chemical | ChemComp-SO4 / | #3: 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: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 57687 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.1 / % possible all: 95.5 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 40 Å / Num. measured all: 469429 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.354 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QK8 Resolution: 1.5→40 Å / SU B: 1.992 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Details: CNS USED IN INITIAL STAGES
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Displacement parameters | Biso mean: 19.265 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.207 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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