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- PDB-2ldm: Solution structure of human PHF20 Tudor2 domain bound to a p53 se... -

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Basic information

Entry
Database: PDB / ID: 2ldm
TitleSolution structure of human PHF20 Tudor2 domain bound to a p53 segment containing a dimethyllysine analog p53K370me2
ComponentsUncharacterized protein
KeywordsTRANSCRIPTION/PROTEIN BINDING / PHF20 / Tudor domain / Epigenetics / methylated p53 / transcription factor / TRANSCRIPTION-PROTEIN BINDING complex
Function / homologySH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCui, G. / Botuyan, M. / Mer, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.
Authors: Cui, G. / Park, S. / Badeaux, A.I. / Kim, D. / Lee, J. / Thompson, J.R. / Yan, F. / Kaneko, S. / Yuan, Z. / Botuyan, M.V. / Bedford, M.T. / Cheng, J.Q. / Mer, G.
History
DepositionMay 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Oct 3, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,0701
Polymers9,0701
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 9070.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-13C HSQC aliphatic
1422D 1H-13C HSQC aromatic
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D HBHA(CO)NH
1823D HN(CA)CO
1923D CCH-TOCSY
11022D (HB)CB(CGCD)HD
11122D (HB)CB(CGCDCE)HE
11213D 1H-15N NOESY
11323D 1H-15N NOESY
11423D 1H-13C NOESY aliphatic
11523D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein, 25 mM sodium phosphate, 0.3 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 0.3 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 15N]1
25 mMsodium phosphate-21
0.3 mMDSS-31
1 mMprotein-4[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-52
0.3 mMDSS-62
Sample conditionsIonic strength: 0.025 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
NMRViewJohnson, One Moon Scientificpeak picking
SANEDuggan, Legge, Dyson & Wrightdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3022 / NOE intraresidue total count: 479 / NOE long range total count: 666 / NOE medium range total count: 260 / NOE sequential total count: 476 / Hydrogen bond constraints total count: 27 / Protein chi angle constraints total count: 40 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 32 / Protein psi angle constraints total count: 33
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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