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Yorodumi- PDB-1fzv: THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 (PLGF-1),... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fzv | ||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 (PLGF-1), AN ANGIOGENIC PROTEIN AT 2.0A RESOLUTION | ||||||
Components | PLACENTA GROWTH FACTOR | ||||||
Keywords | HORMONE/GROWTH FACTOR / cysteine-knot family / growth factor / angiogenesis / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / positive regulation of cell division / vascular endothelial growth factor receptor signaling pathway ...VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / positive regulation of cell division / vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell proliferation / growth factor activity / positive regulation of angiogenesis / cell-cell signaling / heparin binding / cell differentiation / response to hypoxia / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Iyer, S. / Leonidas, D.D. / Swaminathan, G.J. / Maglione, D. / Battisti, M. / Tucci, M. / Persico, M.G. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The crystal structure of human placenta growth factor-1 (PlGF-1), an angiogenic protein, at 2.0 A resolution. Authors: Iyer, S. / Leonidas, D.D. / Swaminathan, G.J. / Maglione, D. / Battisti, M. / Tucci, M. / Persico, M.G. / Acharya, K.R. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Isolation of a human placenta cDNA coding for a protein related to the vascular permeability factor Authors: Magloine, D. / Guerriero, V. / Viglietto, G. / Delli-Bovi, P. / Persico, M.G. #2: Journal: Lab.Invest. / Year: 1997 Title: Placenta Growth Factor-1 is Chemotactic, Mitogenic, and Angiogenic Authors: Ziche, M. / Maglione, D. / Ribatti, D. / Morbidelli, L. / Lago, C.T. / Battisti, M. / Paoletti, I. / Barra, A. / Tucci, M. / Parise, G. / Vincenti, V. / Granger, H.J. / Viglietto, G. / Persico, M.G. #3: Journal: Farmaco / Year: 2000 Title: Recombinant production of PlGF-1 and its activity in animal models. Authors: Maglione, D. / Battisti, M. / Tucci, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fzv.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fzv.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzv_validation.pdf.gz | 387.6 KB | Display | wwPDB validaton report |
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Full document | 1fzv_full_validation.pdf.gz | 390.7 KB | Display | |
Data in XML | 1fzv_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1fzv_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzv ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzv | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | Chain A and Chain B of the molecule form a Homodimer which is the biological unit of this protein. |
-Components
#1: Protein | Mass: 14872.065 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P49763 #2: Chemical | #3: 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: 2.77 Å3/Da / Density % sol: 55.57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, MPD and Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 16K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.5 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 21945 / Num. obs: 20658 / % possible obs: 94.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.67 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.364 / Num. unique all: 2075 / % possible all: 90.4 |
Reflection | *PLUS Num. measured all: 161044 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Resolution: 2→39.17 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 223442.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.2 Å2 / ksol: 0.452 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 3.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.5 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.463 / % reflection Rfree: 4.1 % / Rfactor Rwork: 0.382 |