+Open data
-Basic information
Entry | Database: PDB / ID: 1jnd | |||||||||
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Title | Crystal structure of imaginal disc growth factor-2 | |||||||||
Components | Imaginal disc growth factor-2 | |||||||||
Keywords | HORMONE/GROWTH FACTOR / IDGF / imaginal disc / growth factor / chitinase / insulin receptor / heparin / HORMONE-GROWTH FACTOR COMPLEX | |||||||||
Function / homology | Function and homology information imaginal disc growth factor receptor binding / imaginal disc development / Neutrophil degranulation / chitin catabolic process / chitin binding / carbohydrate metabolic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Varela, P.F. / Llera, A.S. / Mariuzza, R.A. / Tormo, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of imaginal disc growth factor-2. A member of a new family of growth-promoting glycoproteins from Drosophila melanogaster. Authors: Varela, P.F. / Llera, A.S. / Mariuzza, R.A. / Tormo, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jnd.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jnd.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jnd_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 1jnd_full_validation.pdf.gz | 774.1 KB | Display | |
Data in XML | 1jnd_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1jnd_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/1jnd ftp://data.pdbj.org/pub/pdb/validation_reports/jn/1jnd | HTTPS FTP |
-Related structure data
Related structure data | 1jneC 1ctnS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46952.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: 4092089, UniProt: Q9V3D4*PLUS |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.66 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9464 / Wavelength: 0.9464 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. obs: 129904 / % possible obs: 90.3 % / Redundancy: 1.1 % / Rsym value: 0.023 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 1.76 % / Mean I/σ(I) obs: 2.88 / Rsym value: 0.257 / % possible all: 53.5 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 758311 / Rmerge(I) obs: 0.023 |
Reflection shell | *PLUS % possible obs: 53.5 % / Rmerge(I) obs: 0.257 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CTN Resolution: 1.3→100 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 1.8 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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