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- PDB-2lmr: Solution structure of the first sam domain of odin -

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Basic information

Entry
Database: PDB / ID: 2lmr
TitleSolution structure of the first sam domain of odin
ComponentsAnkyrin repeat and SAM domain-containing protein 1A
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


substrate-dependent cell migration / neuron remodeling / ephrin receptor signaling pathway / ephrin receptor binding / neuron projection / nucleoplasm / cytosol
Similarity search - Function
Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Transcription Factor, Ets-1 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / SAM domain profile. ...Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Transcription Factor, Ets-1 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / DNA polymerase; domain 1 / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat and SAM domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsLeone, M. / Mercurio, F.
CitationJournal: Biochemistry / Year: 2012
Title: Solution Structure of the First Sam Domain of Odin and Binding Studies with the EphA2 Receptor.
Authors: Mercurio, F.A. / Marasco, D. / Pirone, L. / Pedone, E.M. / Pellecchia, M. / Leone, M.
History
DepositionDec 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.3May 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: Ankyrin repeat and SAM domain-containing protein 1A


Theoretical massNumber of molelcules
Total (without water)11,3091
Polymers11,3091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Ankyrin repeat and SAM domain-containing protein 1A / Odin


Mass: 11308.677 Da / Num. of mol.: 1 / Fragment: SAM 1 domain residues 691-770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKS1A, ANKS1, KIAA0229, ODIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q92625

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-1H TOCSY
1422D 1H-1H NOESY
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCA
1813D HN(CA)CB
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9-1 mM [U-100% 13C; U-100% 15N] protein, 2.7 mM potassium chloride, 1.8 mM potassium phosphate, 140 mM sodium chloride, 10 mM sodium phosphate, 0.2 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.9-1 mM [U-100% 15N] protein, 2.7 mM potassium chloride, 1.8 mM potassium phosphate, 140 mM sodium chloride, 10 mM sodium phosphate, 0.2 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 13C; U-100% 15N]0.9-11
2.7 mMpotassium chloride-21
1.8 mMpotassium phosphate-31
140 mMsodium chloride-41
10 mMsodium phosphate-51
0.2 %sodium azide-61
mMentity-7[U-100% 15N]0.9-12
2.7 mMpotassium chloride-82
1.8 mMpotassium phosphate-92
140 mMsodium chloride-102
10 mMsodium phosphate-112
0.2 %sodium azide-122
Sample conditionsIonic strength: 0.2 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
VnmrJVarianprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated with cyana without further refinement
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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