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- PDB-1exz: STRUCTURE OF STEM CELL FACTOR -

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Basic information

Entry
Database: PDB / ID: 1exz
TitleSTRUCTURE OF STEM CELL FACTOR
ComponentsSTEM CELL FACTOR
KeywordsHORMONE/GROWTH FACTOR / scf / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


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
Stem cell factor / Stem cell factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SAMARIUM (III) ION / Kit ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsZhang, Z. / Zhang, R. / Joachimiak, A. / Schlessinger, J. / Kong, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of human stem cell factor: implication for stem cell factor receptor dimerization and activation.
Authors: Zhang, Z. / Zhang, R. / Joachimiak, A. / Schlessinger, J. / Kong, X.P.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEM CELL FACTOR
B: STEM CELL FACTOR
C: STEM CELL FACTOR
D: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,83311
Polymers64,0294
Non-polymers8047
Water2,378132
1
A: STEM CELL FACTOR
B: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3555
Polymers32,0152
Non-polymers3413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-36 kcal/mol
Surface area14630 Å2
MethodPISA
2
C: STEM CELL FACTOR
D: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4786
Polymers32,0152
Non-polymers4634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-13 kcal/mol
Surface area13680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-65 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.154, 87.526, 79.434
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
STEM CELL FACTOR / SCF


Mass: 16007.306 Da / Num. of mol.: 4 / Fragment: 26-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P21583
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 400, 250 mM CaCl2, 1 mM SmCl3, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
225-30 %PEG4001reservoir
30.25 M1reservoirCaCl2
40.1 MHEPES1reservoir
51 mM1dropSmCl3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID11.03
SYNCHROTRONAPS 19-ID21.55
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.031
21.551
ReflectionResolution: 2.3→40 Å / Num. all: 21877 / Num. obs: 21454 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7 % / Rmerge(I) obs: 0.25 / % possible all: 90.1
Reflection shell
*PLUS
% possible obs: 90.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNSrefinement
RefinementResolution: 2.3→40 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: mlf / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2133 -randomly selected 10% of reflections
Rwork0.223 ---
all0.223 21877 --
obs0.223 21494 10 %-
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 14 132 4236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.22

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