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Open data
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Basic information
Entry | Database: PDB / ID: 1scf | ||||||
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Title | HUMAN RECOMBINANT STEM CELL FACTOR | ||||||
![]() | STEM CELL FACTOR | ||||||
![]() | HORMONE/GROWTH FACTOR / HUMAN STEM CELL FACTOR / STEEL FACTOR / KIT LIGAND / MAST CELL GROWTH FACTOR / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | ![]() positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / positive regulation of hematopoietic stem cell proliferation / melanocyte migration / myeloid leukocyte differentiation / positive regulation of melanocyte differentiation / positive regulation of mast cell proliferation ...positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / positive regulation of hematopoietic stem cell proliferation / melanocyte migration / myeloid leukocyte differentiation / positive regulation of melanocyte differentiation / positive regulation of mast cell proliferation / mast cell apoptotic process / mast cell proliferation / positive regulation of Ras protein signal transduction / neural crest cell migration / positive regulation of leukocyte migration / embryonic hemopoiesis / Regulation of KIT signaling / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / T cell proliferation / positive regulation of T cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / filopodium / cytokine activity / growth factor activity / Signaling by SCF-KIT / response to organic cyclic compound / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / lamellipodium / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Ras protein signal transduction / cytoskeleton / cell adhesion / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, X. / Gurel, O. / Langley, K.E. / Hendrickson, W.A. | ||||||
![]() | ![]() Title: Structure of the active core of human stem cell factor and analysis of binding to its receptor kit. Authors: Jiang, X. / Gurel, O. / Mendiaz, E.A. / Stearns, G.W. / Clogston, C.L. / Lu, H.S. / Osslund, T.D. / Syed, R.S. / Langley, K.E. / Hendrickson, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.3 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400 KB | Display | ![]() |
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Full document | ![]() | 410.2 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 31074.225 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-1PE / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | pH: 7.4 / Details: pH 7.40 | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 65689 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.056 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.23 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.581 / % possible all: 72 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 72 % / Rmerge(I) obs: 0.581 |
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Processing
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Refinement | Method to determine structure: ![]() Details: REFINEMENT WAS PERFORMED WITH ANOMALOUS ON; PARAM19_MOD.PRO AND TOPH19_MOD.PRO ARE MODIFIED PARAMETER AND TOPOLOGY FILES OF PARAM19.PRO AND TOPH19.PRO, RESPECTIVELY, FOR SELENOMETHIONYL ...Details: REFINEMENT WAS PERFORMED WITH ANOMALOUS ON; PARAM19_MOD.PRO AND TOPH19_MOD.PRO ARE MODIFIED PARAMETER AND TOPOLOGY FILES OF PARAM19.PRO AND TOPH19.PRO, RESPECTIVELY, FOR SELENOMETHIONYL PROTEINS. NCS RESTRAINTS WERE APPLIED ONLY DURING THE INITIAL REFINEMENT.
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Displacement parameters | Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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