+Open data
-Basic information
Entry | Database: PDB / ID: 2luu | ||||||
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Title | NMR solution structure of midkine-b, mdkb | ||||||
Components | Midkine-related growth factor Mdk2 | ||||||
Keywords | HORMONE / beta sheet / independent half-domain / disulfide bond | ||||||
Function / homology | Function and homology information neural crest formation / positive regulation of cell division / positive regulation of neuron differentiation / brain development / growth factor activity / heparin binding / nervous system development / extracellular region Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Yang, D. / Lim, J. / Meng, D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2luu.cif.gz | 443.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2luu.ent.gz | 378.4 KB | Display | PDB format |
PDBx/mmJSON format | 2luu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/2luu ftp://data.pdbj.org/pub/pdb/validation_reports/lu/2luu | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Independent half-domains enriched with disulfide bonds and separated by linker. | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: NOE distance refinement using CYANA 2.1. Hydrogen bond restraints using H-D exchange experiment | ||||||||||||||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Average 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 rms | Distance rms dev: 1.07 Å / Distance rms dev error: 0.24 Å |