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- PDB-2luu: NMR solution structure of midkine-b, mdkb -

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Basic information

Entry
Database: PDB / ID: 2luu
TitleNMR solution structure of midkine-b, mdkb
ComponentsMidkine-related growth factor Mdk2
KeywordsHORMONE / beta sheet / independent half-domain / disulfide bond
Function / homology
Function and homology information


Signaling by ALK / MDK and PTN in ALK signaling / neural crest formation / positive regulation of cell division / positive regulation of neuron differentiation / growth factor activity / brain development / nervous system development / heparin binding / extracellular region
Similarity search - Function
Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily / Pleiotrophin/Midkine, C-terminal domain superfamily / PTN/MK heparin-binding protein family, C-terminal domain / PTN/MK heparin-binding protein family, N-terminal domain / Pleiotrophin / midkine family
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, D. / Lim, J. / Meng, D.
CitationJournal: Biochem.J. / Year: 2013
Title: Structure-function analysis of full-length midkine reveals novel residues important for heparin binding and zebrafish embryogenesis.
Authors: Lim, J. / Yao, S. / Graf, M. / Winkler, C. / Yang, D.
History
DepositionJun 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Oct 9, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Midkine-related growth factor Mdk2


Theoretical massNumber of molelcules
Total (without water)14,0211
Polymers14,0211
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)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Midkine-related growth factor Mdk2 / Uncharacterized protein


Mass: 14021.163 Da / Num. of mol.: 1 / Fragment: UNP residues 22-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdkb, mdk2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DDG2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Independent half-domains enriched with disulfide bonds and separated by linker.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CO)CA
1413D HNCA
1513D MQ-(H)CCH-TOCSY
1614D timeshared 13C/ 15N edited NOESY

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Sample preparation

DetailsContents: 10 mM potassium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphate-11
0.1 mMsodium azide-21
100 mMsodium chloride-31
1 mMEDTA-41
0.8 mMentity-5[U-100% 13C; U-100% 15N]1
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
NMRspyZheng Yu and Yang Daiwenchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRPipe1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOE distance refinement using CYANA 2.1. Hydrogen bond restraints using H-D exchange experiment
NMR constraintsNOE constraints total: 1412 / NOE intraresidue total count: 772 / NOE long range total count: 311 / NOE medium range total count: 69 / NOE sequential total count: 260 / Hydrogen bond constraints total count: 12 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 49
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 3.2 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 3.8 ° / Maximum upper distance constraint violation: 0.42 Å / Torsion angle constraint violation method: CYANA 2.1
NMR ensemble rmsDistance rms dev: 1.07 Å / Distance rms dev error: 0.24 Å

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