+Open data
-Basic information
Entry | Database: PDB / ID: 7nbi | ||||||
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Title | Crystal structure of a monomeric FLT3 Ligand variant | ||||||
Components | Fms-related tyrosine kinase 3 ligand | ||||||
Keywords | DE NOVO PROTEIN / FLT3 Ligand / Engineered cytokine / monomeric FLT3 ligand | ||||||
Function / homology | Function and homology information STAT5 Activation / FLT3 signaling through SRC family kinases / embryonic hemopoiesis / PI3K Cascade / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / FLT3 Signaling / cytokine activity / receptor tyrosine kinase binding / Constitutive Signaling by Aberrant PI3K in Cancer ...STAT5 Activation / FLT3 signaling through SRC family kinases / embryonic hemopoiesis / PI3K Cascade / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / FLT3 Signaling / cytokine activity / receptor tyrosine kinase binding / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / signaling receptor binding / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Pannecoucke, E. / Raes, L. / Savvides, S.N. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Engineering and crystal structure of a monomeric FLT3 ligand variant. Authors: Pannecoucke, E. / Raes, L. / Savvides, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nbi.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nbi.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 7nbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nbi_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 7nbi_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 7nbi_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 7nbi_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/7nbi ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nbi | HTTPS FTP |
-Related structure data
Related structure data | 1eteS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15875.146 Da / Num. of mol.: 2 / Mutation: L33D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLT3LG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami B / References: UniProt: P49771 #2: Chemical | ChemComp-SO4 / #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: 1.78 Å3/Da / Density % sol: 30.89 % / Description: Morphologically twinned |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.0 M ammonium sulfate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→18.64 Å / Num. obs: 70278 / % possible obs: 94.9 % / Redundancy: 8.81 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.077 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 2.37 % / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4053 / CC1/2: 0.728 / Rrim(I) all: 0.567 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ETE Resolution: 1.65→18.42 Å / SU ML: 0.1961 / Cross valid method: FREE R-VALUE / Phase error: 22.5253 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→18.42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.80387887907 Å / Origin y: 34.3372772444 Å / Origin z: 52.6374430596 Å
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Refinement TLS group | Selection details: all |