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Open data
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Basic information
Entry | Database: PDB / ID: 1o6j | ||||||
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Title | Tryparedoxin II from C.fasciculata solved by sulphur phasing | ||||||
![]() | TRYPAREDOXIN II | ||||||
![]() | ELECTRON TRANSPORT / TRYPAREDOXIN II / SULPHUR PHASING / SAD / S-SAD | ||||||
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: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for ...Title: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for Solving Protein Crystal Structures Authors: Micossi, E. / Hunter, W.N. / Leonard, G.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 16928.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | CONSTRUCT STARTS AT RESIDUE 16 | |
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-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 Temperature: 277 K / 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: 1.77 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 Highest resolution: 2.35 Å / Lowest resolution: 40 Å / Num. obs: 35567 / % possible obs: 100 % / Num. measured all: 531442 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.76 Å / % possible obs: 100 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 9.5 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.35→30 Å / SU B: 6.529 / SU ML: 0.16 / 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: 44.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.201 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.351 Å / Lowest resolution: 2.412 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.256 / Num. reflection Rwork: 126 / Total num. of bins used: 20 |