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- PDB-2lku: Solution structure of reduced poplar apo GrxS14 -

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Basic information

Entry
Database: PDB / ID: 2lku
TitleSolution structure of reduced poplar apo GrxS14
ComponentsGrxS14
KeywordsELECTRON TRANSPORT / GrxS14 / glutaredoxin / glutathione
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin domain-containing protein
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, L. / Xia, B.
CitationJournal: To be Published
Title: Solution structure of reduced poplar apo GrxS14
Authors: Wang, L. / Xia, B.
History
DepositionOct 21, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GrxS14


Theoretical massNumber of molelcules
Total (without water)12,1951
Polymers12,1951
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein GrxS14


Mass: 12195.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9IA39*PLUS
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of reduced poplar apo GrxS14
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY aliphatic
1413D 1H-13C NOESY aromatic
1513D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.2 mM [U-13C; U-15N] apo GrxS14 protein-1, 30 mM TRIS-2, 50 mM sodium chloride-3, 20 mM GSH-4, 95 % H2O-5, 5 % [U-2H] D2O-6, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMapo GrxS14 protein-1[U-13C; U-15N]1
30 mMTRIS-21
50 mMsodium chloride-31
20 mMGSH-41
95 %H2O-51
5 %D2O-6[U-2H]1
Sample conditionsIonic strength: 80 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
DYANA3Guntert, Braun and Wuthrichstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
ProcheckNMRLaskowski and MacArthurgeometry optimization
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: using AMBER ff03 force filed refinement
NMR constraintsNOE constraints total: 2561 / NOE intraresidue total count: 918 / NOE long range total count: 211 / NOE medium range total count: 168 / NOE sequential total count: 407
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.09 Å / Maximum upper distance constraint violation: 0.229 Å / Representative conformer: 1

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