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- PDB-1dby: NMR STRUCTURES OF CHLOROPLAST THIOREDOXIN M CH2 FROM THE GREEN AL... -

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Entry
Database: PDB / ID: 1dby
TitleNMR STRUCTURES OF CHLOROPLAST THIOREDOXIN M CH2 FROM THE GREEN ALGA CHLAMYDOMONAS REINHARDTII
ComponentsCHLOROPLAST THIOREDOXIN M CH2
KeywordsOXIDOREDUCTASE / THIOREDOXIN M / THIOREDOXIN CH2 / CHLOROPLASTIC THIOREDOXIN
Function / homology
Function and homology information


protein-disulfide reductase activity / chloroplast
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin M-type, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodSOLUTION NMR / SIMULATED ANNEALING STARTING FROM A RANDOM ARRAY OF ATOMS. HIGH TEMPERATURE SIMULATED ANNEALING. RESTRAINED MOLECULAR DYNAMIC AT ROOM TEMPERATURE.
AuthorsLancelin, 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
DepositionNov 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHLOROPLAST THIOREDOXIN M CH2


Theoretical massNumber of molelcules
Total (without water)11,6871
Polymers11,6871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY. STRUCTURES WITH FAVORABLE NON- BOND ENERGY. STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS. STRUCTURES WITH THE LOWEST ENERGY.
RepresentativeModel #16closest to the average

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Components

#1: Protein CHLOROPLAST THIOREDOXIN M CH2


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D-SEPARATED-TOCSY
1322D NOESY
1432D NOESY
152TOCSY
NMR detailsText: 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
Solution-IDContents
12-3 MM THIOREDOXIN M (OXIDIZED) U-15N; 100 MM POTASSIUM PHOSPHATE BUFFER PH 5.8; 90% H2O 10% D20
22-3 MM THIOREDOXIN M (OXIDIZED);100 MM POTASSIUM PHOSPHATE BUFFER PH 5.8; 90% H2O 10% D20
32-3 MM THIOREDOXIN M (OXIDIZED);100 MM POTASSIUM PHOSPHATE BUFFER PH 5.8; 100% D20
Sample conditionsIonic strength: 100 mM POTASSIUM PHOSPHATE / pH: 5.8 / Pressure: AMBIENT / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2BRUKER SPECTROSPIN AGcollection
Felix2.3BIOSYM TECHNOLOGIESdata analysis
NMRPipe1.7DELAGLIOprocessing
Discover2.3.0BIOSYM TECHNOLOGIESstructure solution
UXNMR940501.3BRUKER SPECTROSPIN AGcollection
Gifa4DELSUCprocessing
Discover2.3.0BIOSYM TECHNOLOGIESrefinement
RefinementMethod: 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 representativeSelection criteria: closest to the average
NMR ensembleConformer 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

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