+Open data
-Basic information
Entry | Database: PDB / ID: 3hal | ||||||
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Title | Crystal structure of Rabbit acidic fibroblast growth factor | ||||||
Components | Fibroblast growth factor 1 isoform 1 | ||||||
Keywords | HORMONE / beta-trefoil | ||||||
Function / homology | Function and homology information : / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / organ induction / S100 protein binding / positive regulation of sprouting angiogenesis / positive regulation of cell division ...: / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / organ induction / S100 protein binding / positive regulation of sprouting angiogenesis / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / positive regulation of epithelial cell proliferation / growth factor activity / lung development / wound healing / integrin binding / heparin binding / cellular response to heat / cell cortex / angiogenesis / cell differentiation / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Blaber, M. / Lee, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: X-ray structure and biophysical properties of rabbit fibroblast growth factor 1. Authors: Lee, J. / Blaber, S.I. / Irsigler, A. / Aspinwall, E. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hal.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hal.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3hal ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3hal | HTTPS FTP |
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-Related structure data
Related structure data | 1jqzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16605.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: FGF1 / Plasmid: PET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7NZB1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG4000, 0.1M Na HEPES (pH7.5), 0.2M NaOAc, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.43 Å / Num. all: 25636 / Num. obs: 24147 / % possible obs: 94.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 22.53 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 36.07 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.93 / Num. unique all: 2538 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JQZ Resolution: 1.8→31.911 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.17 / σ(F): 0.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.95 Å2 / ksol: 0.457 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.65 Å2 / Biso mean: 29.35 Å2 / Biso min: 12.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.911 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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