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Yorodumi- 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 | ||||||
Components | CHLOROPLAST THIOREDOXIN M CH2 | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN M / THIOREDOXIN CH2 / CHLOROPLASTIC THIOREDOXIN | ||||||
Function / homology | Function and homology information glycerol ether metabolic process / protein-disulfide reductase activity / chloroplast / cell redox homeostasis Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING STARTING FROM A RANDOM ARRAY OF ATOMS. HIGH TEMPERATURE SIMULATED ANNEALING. RESTRAINED MOLECULAR DYNAMIC AT ROOM TEMPERATURE. | ||||||
Authors | Lancelin, J.-M. / Guilhaudis, L. / Krimm, I. / Blackledge, M.J. / Marion, D. | ||||||
Citation | Journal: Proteins / Year: 2000 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: Journal: J.Biochem.(Tokyo) / Year: 1993 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: Journal: Plant Mol.Biol. / Year: 1995 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: Journal: Nucleic Acids Res. / Year: 1992 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: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1dby.cif.gz | 889.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dby.ent.gz | 772.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dby_validation.pdf.gz | 356.4 KB | Display | wwPDB validaton report |
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Full document | 1dby_full_validation.pdf.gz | 494.5 KB | Display | |
Data in XML | 1dby_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 1dby_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/1dby ftp://data.pdbj.org/pub/pdb/validation_reports/db/1dby | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Chlamydomonas reinhardtii (plant) / Gene: NUCLEAR / Organelle: CHLOROPLAST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23400 |
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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. |
-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 |