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Open data
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Basic information
Entry | Database: PDB / ID: 1oc8 | ||||||
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Title | TRYPAREDOXIN II FROM C.FASCICULATA SOLVED BY MR | ||||||
![]() | TRYPAREDOXIN II | ||||||
![]() | ELECTRON TRANSPORT / TRYPAREDOXIN II | ||||||
Function / homology | ![]() protein-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leonard, G.A. / Micossi, E. / Hunter, W.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.4 KB | Display | ![]() |
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PDB format | ![]() | 58.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.5 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o73C ![]() 1o7uC ![]() 1o85C ![]() 1o8wC ![]() 1o8xC ![]() 1oc9C ![]() 1qk8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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