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- PDB-2lj9: Partial 3d structure of the c-terminal part of the free arabidops... -

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Basic information

Entry
Database: PDB / ID: 2lj9
TitlePartial 3d structure of the c-terminal part of the free arabidopsis thaliana cp12-2 in its oxidized form
ComponentsCP12 domain-containing protein 2
KeywordsPROTEIN BINDING / HELIX / Intrinsically disordered protein
Function / homology
Function and homology information


peptide cross-linking via L-cystine / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / cellular response to anoxia / response to sucrose / reductive pentose-phosphate cycle / chloroplast stroma / cellular response to cold / nickel cation binding / response to light stimulus ...peptide cross-linking via L-cystine / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / cellular response to anoxia / response to sucrose / reductive pentose-phosphate cycle / chloroplast stroma / cellular response to cold / nickel cation binding / response to light stimulus / chloroplast / cellular response to heat / protein-containing complex assembly / protein-macromolecule adaptor activity / copper ion binding / protein-containing complex binding / enzyme binding / protein-containing complex / cytosol
Similarity search - Function
Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12
Similarity search - Domain/homology
Calvin cycle protein CP12-2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTrivelli, X. / Sparla, F. / Marri, L. / Trost, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Conformational Selection and Folding-upon-binding of Intrinsically Disordered Protein CP12 Regulate Photosynthetic Enzymes Assembly.
Authors: Fermani, S. / Trivelli, X. / Sparla, F. / Thumiger, A. / Calvaresi, M. / Marri, L. / Falini, G. / Zerbetto, F. / Trost, P.
History
DepositionSep 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CP12 domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)10,6431
Polymers10,6431
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CP12 domain-containing protein 2 / CP12 protein-like protein / Putative CP12 protein


Mass: 10643.457 Da / Num. of mol.: 1 / Fragment: UNP residues 54-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g62410, CP12-2, T12C14_110 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LZP9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1252D 1H-13C HSQC
1332D 1H-1H TOCSY
1432D 1H-1H NOESY
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CO)CA
11213D H(CCO)NH
11323D 1H-15N NOESY
11423D 1 15N TOCSY
11542D 1H-1H TOCSY
11642D 1H-1H NOESY
1172HETERONUCLEAR NOE 15N
1181HBHANH
NMR detailsText: STRUCTURE DETERMINED WITH HOMONUCLEAR NOES AND TALOS- DERIVED BACKBONE ANGLES

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] CP12, 5 % [U-2H] D2O, 0.1-0.2 mM TSP, 95 % H2O, 25 mM potassium phosphate, 0.05 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-15N] CP12, 5 % [U-2H] D2O, 0.1-0.2 mM TSP, 95 % H2O, 25 mM potassium phosphate, 0.05 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31 mM CP12, 5 % [U-2H] D2O, 0.1-0.2 mM TSP, 95 % H2O, 25 mM potassium phosphate, 0.05 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
41 mM CP12, 100 % [U-2H] D2O, 0.1-0.2 mM TSP, 25 mM potassium phosphate, 0.05 w/v sodium azide, 100% D2O100% D2O
51 mM [U-100% 13C; U-100% 15N] CP12, 100 % [U-2H] D2O, 0.1-0.2 mM TSP, 25 mM potassium phosphate, 0.05 w/v sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1 mMCP12-2-1[U-13C; U-15N]1
5 %D2O-2[U-2H]1
mMTSP-30.1-0.21
95 %H2O-41
25 mMpotassium phosphate-51
0.05 w/vsodium azide-61
1 mMCP12-2-7[U-15N]2
5 %D2O-8[U-2H]2
mMTSP-90.1-0.22
95 %H2O-102
25 mMpotassium phosphate-112
0.05 w/vsodium azide-122
1 mMCP12-2-133
5 %D2O-14[U-2H]3
mMTSP-150.1-0.23
95 %H2O-163
25 mMpotassium phosphate-173
0.05 w/vsodium azide-183
1 mMCP12-2-194
100 %D2O-20[U-2H]4
mMTSP-210.1-0.24
25 mMpotassium phosphate-224
0.05 w/vsodium azide-234
1 mMCP12-2-24[U-100% 13C; U-100% 15N]5
100 %D2O-25[U-2H]5
mMTSP-260.1-0.25
25 mMpotassium phosphate-275
0.05 w/vsodium azide-285
Sample conditionspH: 7 / Pressure: atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE4003

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Processing

NMR software
NameVersionDeveloperClassification
PROCHECKLASKOWSKI, MACARTHUR, SMITH, JONES, HUTCHINSON, MORRIS, MOSSrefinement
CNSSOLVE1.2.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin1.3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 189 / NOE intraresidue total count: 75 / NOE long range total count: 2 / NOE medium range total count: 37 / NOE sequential total count: 75 / Hydrogen bond constraints total count: 2 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.1097 Å / Distance rms dev error: 0.0118 Å

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