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- PDB-3uf5: Crystal structure of the mouse Colony-Stimulating Factor 1 (mCSF-... -

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Basic information

Entry
Database: PDB / ID: 3uf5
TitleCrystal structure of the mouse Colony-Stimulating Factor 1 (mCSF-1) cytokine
ComponentsMacrophage colony-stimulating factor 1
KeywordsCYTOKINE / Hematopoietic cytokine / RTKIII / Four-helix bundle
Function / homology
Function and homology information


Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / developmental process involved in reproduction / positive regulation of odontogenesis of dentin-containing tooth / CSF1-CSF1R complex ...Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / developmental process involved in reproduction / positive regulation of odontogenesis of dentin-containing tooth / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of mononuclear cell proliferation / positive regulation of mononuclear cell migration / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of multicellular organism growth / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / positive regulation of Ras protein signal transduction / positive regulation of macrophage proliferation / branching involved in mammary gland duct morphogenesis / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / positive regulation of macrophage chemotaxis / monocyte differentiation / macrophage differentiation / regulation of ossification / homeostasis of number of cells within a tissue / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of protein metabolic process / ossification / osteoclast differentiation / cytokine activity / response to ischemia / growth factor activity / Ras protein signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsElegheert, J. / Bracke, N. / Bekaert, A. / Savvides, S.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1
Authors: Elegheert, J. / Bracke, N. / Pouliot, P. / Gutsche, I. / Shkumatov, A.V. / Tarbouriech, N. / Verstraete, K. / Bekaert, A. / Burmeister, W.P. / Svergun, D.I. / Lambrecht, B.N. / Vergauwen, B. / Savvides, S.N.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage colony-stimulating factor 1
B: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9056
Polymers35,7442
Non-polymers1604
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-35 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.320, 68.690, 144.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macrophage colony-stimulating factor 1 / CSF-1 / MCSF / Processed macrophage colony-stimulating factor 1


Mass: 17872.107 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csf1, Csfm / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P07141
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 20% PEG 6000, 0.2M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9726 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 9314 / Num. obs: 9314 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.95 Å / % possible all: 98.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_874) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.459 Å / SU ML: 0.72 / σ(F): 2 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 931 10 %random
Rwork0.2097 ---
obs0.2144 9312 98.48 %-
all-9312 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.146 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-39.3982 Å2-0 Å2-0 Å2
2---10.3431 Å2-0 Å2
3----29.0551 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 4 28 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032419
X-RAY DIFFRACTIONf_angle_d0.5453244
X-RAY DIFFRACTIONf_dihedral_angle_d13.252906
X-RAY DIFFRACTIONf_chiral_restr0.037358
X-RAY DIFFRACTIONf_plane_restr0.002427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.94770.39981280.30991148X-RAY DIFFRACTION98
2.9477-3.13240.32571320.28111188X-RAY DIFFRACTION99
3.1324-3.37410.32021310.23711180X-RAY DIFFRACTION99
3.3741-3.71340.25581320.2051188X-RAY DIFFRACTION99
3.7134-4.25020.2211320.17461189X-RAY DIFFRACTION99
4.2502-5.35270.26021360.17851220X-RAY DIFFRACTION98
5.3527-39.46290.20471400.20531268X-RAY DIFFRACTION97

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