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- PDB-7cco: The binding structure of a lanthanide binding tag (LBT3) with lan... -

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Basic information

Entry
Database: PDB / ID: 7cco
TitleThe binding structure of a lanthanide binding tag (LBT3) with lanthanum ion (La3+)
ComponentsLBT3
KeywordsDE NOVO PROTEIN / Lanthanide-Binding Peptide Lanthanum ion
Function / homologyLANTHANUM (III) ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHatanaka, T. / Kikkawa, N. / Matsugami, A. / Hosokawa, Y. / Hayashi, F. / Ishida, N.
CitationJournal: Sci Rep / Year: 2020
Title: The origins of binding specificity of a lanthanide ion binding peptide.
Authors: Hatanaka, T. / Kikkawa, N. / Matsugami, A. / Hosokawa, Y. / Hayashi, F. / Ishida, N.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LBT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0612
Polymers1,9221
Non-polymers1391
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area220 Å2
ΔGint-11 kcal/mol
Surface area1700 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide LBT3


Mass: 1922.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 400 uM LBT3, 800 uM LANTHANUM (III) ION, 30 mM [U-99% 2H] MES, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMLBT3natural abundance1
800 uMLANTHANUM (III) IONnatural abundance1
30 mMMES[U-99% 2H]1
Sample conditionsIonic strength: 30-100 mM / Label: 1 / pH: 6 / PH err: 0.1 / Pressure: ambient atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.structure calculation
GROMACSJustin A. Lemkul,refinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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