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Open data
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Basic information
Entry | Database: PDB / ID: 1oc9 | ||||||
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Title | TRYPAREDOXIN II FROM C.FASCICULATA solved by MR | ||||||
![]() | (TRYPAREDOXIN II) x 2 | ||||||
![]() | 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 | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 443.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o73C ![]() 1o7uC ![]() 1o85C ![]() 1o8wC ![]() 1o8xC ![]() 1oc8SC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.769, 0.404, -0.495), Vector: |
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Components
#1: Protein | Mass: 17121.619 Da / Num. of mol.: 1 / Fragment: RESIDUES 16-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 17163.721 Da / Num. of mol.: 1 / Fragment: RESIDUES 16-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
Sequence details | CONSTRUCT STARTS AT RESIDUE 16 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||
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: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 28025 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 9.6 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 4.9 % / Num. measured all: 136117 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OC8 Resolution: 2.35→30 Å / SU B: 6.393 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / Details: CNS USED IN INITIAL STAGES
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Displacement parameters | Biso mean: 44.113 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refinement | *PLUS Rfactor Rfree: 0.213 / Rfactor Rwork: 0.196 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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