+Open data
-Basic information
Entry | Database: PDB / ID: 1oc9 | ||||||
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Title | TRYPAREDOXIN II FROM C.FASCICULATA solved by MR | ||||||
Components | (TRYPAREDOXIN II) x 2 | ||||||
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: 2.35 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 | 1oc9.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oc9.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1oc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1oc9 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1oc9 | HTTPS FTP |
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-Related structure data
Related structure data | 1o73C 1o7uC 1o85C 1o8wC 1o8xC 1oc8SC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.769, 0.404, -0.495), Vector: |
-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.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O77093 |
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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.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O77093 |
#3: Water | ChemComp-HOH / |
Sequence details | CONSTRUCT STARTS AT RESIDUE 16 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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