+Open data
-Basic information
Entry | Database: PDB / ID: 6svk | ||||||
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Title | human Myeloid-derived growth factor (MYDGF) | ||||||
Components | Myeloid-derived growth factor | ||||||
Keywords | CYTOKINE / MYDGF / growth factor / orphan ligand / ischemic tissue repair / unique cytokine fold / reduces scar size after myocardial infarction | ||||||
Function / homology | Function and homology information XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process ...XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.604 Å | ||||||
Authors | Ebenhoch, R. / Nar, H. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Crystal structure and receptor-interacting residues of MYDGF - a protein mediating ischemic tissue repair. Authors: Ebenhoch, R. / Akhdar, A. / Reboll, M.R. / Korf-Klingebiel, M. / Gupta, P. / Armstrong, J. / Huang, Y. / Frego, L. / Rybina, I. / Miglietta, J. / Pekcec, A. / Wollert, K.C. / Nar, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6svk.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6svk.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 6svk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/6svk ftp://data.pdbj.org/pub/pdb/validation_reports/sv/6svk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15854.741 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYDGF, C19orf10 / Production host: Homo sapiens (human) / Strain (production host): HEK 293-6E / References: UniProt: Q969H8 #2: Chemical | ChemComp-MLI / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 48% M1K3350 (12% w/v PEG 1000, 12% w/v PEG 3350, and 12% v/v MPD, original solution Molecular Dimensions), 1,25% NPS (3.75 mM sodium nitrate, 3.75 mM sodium phosphate dibasic, and 3.75 mM ...Details: 48% M1K3350 (12% w/v PEG 1000, 12% w/v PEG 3350, and 12% v/v MPD, original solution Molecular Dimensions), 1,25% NPS (3.75 mM sodium nitrate, 3.75 mM sodium phosphate dibasic, and 3.75 mM ammonium sulfate; original solution MolecularDimensions), 0.1M MMT buffer (pH 6.4) (0.02 M DL-malic acid, 0.04 M MES monohydrate, 0.04 M Tris) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.604→42.155 Å / Num. obs: 28207 / % possible obs: 85.1 % / Redundancy: 19.1 % / Biso Wilson estimate: 17.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rsym value: 0.215 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.604→1.707 Å / Redundancy: 15 % / Rmerge(I) obs: 2.299 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1409 / CC1/2: 0.51 / Rsym value: 2.299 / % possible all: 25.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.604→42.155 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.119
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Displacement parameters | Biso max: 99.56 Å2 / Biso mean: 19.67 Å2 / Biso min: 7.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.604→42.155 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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