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- PDB-1dby: NMR STRUCTURES OF CHLOROPLAST THIOREDOXIN M CH2 FROM THE GREEN AL... -
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Basic information
Entry | Database: PDB / ID: 1dby | ||||||
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Title | NMR STRUCTURES OF CHLOROPLAST THIOREDOXIN M CH2 FROM THE GREEN ALGA CHLAMYDOMONAS REINHARDTII | ||||||
![]() | CHLOROPLAST THIOREDOXIN M CH2 | ||||||
![]() | OXIDOREDUCTASE / THIOREDOXIN M / THIOREDOXIN CH2 / CHLOROPLASTIC THIOREDOXIN | ||||||
Function / homology | ![]() glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis / chloroplast Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING STARTING FROM A RANDOM ARRAY OF ATOMS. HIGH TEMPERATURE SIMULATED ANNEALING. RESTRAINED MOLECULAR DYNAMIC AT ROOM TEMPERATURE. | ||||||
![]() | Lancelin, J.-M. / Guilhaudis, L. / Krimm, I. / Blackledge, M.J. / Marion, D. | ||||||
![]() | ![]() Title: NMR structures of thioredoxin m from the green alga Chlamydomonas reinhardtii. Authors: Lancelin, J.M. / Guilhaudis, L. / Krimm, I. / Blackledge, M.J. / Marion, D. / Jacquot, J.P. #1: ![]() Title: Secondary Structure and Protein Folding of Recombinant Chloroplastic Thioredoxin Ch2 from the Green Alga Chlamydomonas reinhardtii as Determined by 1H NMR Authors: Lancelin, J.-M. / Stein, M. / Jacquot, J.-P. #2: ![]() Title: Chlamydomonas reinhardtii Thioredoxins: Structure of the Genes Coding for Chloroplastic m and Cytosolic h Isoforms; Expression in Escherichia coli of the Recombinant Proteins, Purification and ...Title: Chlamydomonas reinhardtii Thioredoxins: Structure of the Genes Coding for Chloroplastic m and Cytosolic h Isoforms; Expression in Escherichia coli of the Recombinant Proteins, Purification and Biochemical Properties Authors: Stein, M. / Jacquot, J.-P. / Jeannette, E. / Decottignies, P. / Hodges, M. / Lancelin, J.-M. / Mittard, V. / Schmitter, J.M. / Miginiac-Maslow, M. #3: ![]() Title: PCR Cloning of a Nucleotidic Sequence Coding for the Mature Part of Chlamydomonas reinhardtii Thioredoxin Ch2 Authors: Jacquot, J.-P. / Stein, M. / Hodges, M. / Miginiac-Maslow, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 889.3 KB | Display | ![]() |
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PDB format | ![]() | 772.4 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 356.4 KB | Display | ![]() |
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Full document | ![]() | 494.5 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 71.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 11686.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR IN H20 AND 100% D2O AND 3D- 15N SEPARATED NOESY AND TOCSY DATA. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM POTASSIUM PHOSPHATE / pH: 5.8 / Pressure: AMBIENT / Temperature: 311 K | ||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING STARTING FROM A RANDOM ARRAY OF ATOMS. HIGH TEMPERATURE SIMULATED ANNEALING. RESTRAINED MOLECULAR DYNAMIC AT ROOM TEMPERATURE. Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 1372 TOTAL INTERPROTON DISTANCE RESTRAINTS, 1348 ARE DERIVED FROM NOE DATA AND 44 DERIVED FROM SLOW DEUTERIUM EXCHANGE EXPERIMENTS OF HYDROGEN BONDED AMIDE ...Details: THE STRUCTURES ARE BASED ON 1372 TOTAL INTERPROTON DISTANCE RESTRAINTS, 1348 ARE DERIVED FROM NOE DATA AND 44 DERIVED FROM SLOW DEUTERIUM EXCHANGE EXPERIMENTS OF HYDROGEN BONDED AMIDE PROTONS IN REGULAR SECONDARY STRUCTURE MOTIFS. THE RESTRAINT SET INCLUDES 102 DIHEDRAL RESTRAINTS, 66 PHI, 34 KHI1, 2 KHI2. FINAL STRUCTURES ARE REFINED AGAINST THE FULL DESCRIPTION OF AMBER4 FORCE FIELD WITH REDUCED CHARGES FOR FORMALLY CHARGED GROUPS AS ARG, LYS, ASP, GLU RESIDUES. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY. STRUCTURES WITH FAVORABLE NON- BOND ENERGY. STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS. STRUCTURES WITH THE LOWEST ENERGY. Conformers calculated total number: 50 / Conformers submitted total number: 28 |