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- PDB-1lki: THE CRYSTAL STRUCTURE AND BIOLOGICAL FUNCTION OF LEUKEMIA INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 1lki
TitleTHE CRYSTAL STRUCTURE AND BIOLOGICAL FUNCTION OF LEUKEMIA INHIBITORY FACTOR: IMPLICATIONS FOR RECEPTOR BINDING
ComponentsLEUKEMIA INHIBITORY FACTOR
KeywordsCYTOKINE / FOUR HELIX BUNDLE
Function / homology
Function and homology information


leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / transdifferentiation / IL-6-type cytokine receptor ligand interactions / negative regulation of meiotic nuclear division / positive regulation of corticotropin secretion / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT ...leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / transdifferentiation / IL-6-type cytokine receptor ligand interactions / negative regulation of meiotic nuclear division / positive regulation of corticotropin secretion / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT / leukemia inhibitory factor signaling pathway / lung vasculature development / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of hormone secretion / trophoblast giant cell differentiation / positive regulation of peptidyl-serine phosphorylation of STAT protein / lung lobe morphogenesis / positive regulation of macrophage differentiation / positive regulation of astrocyte differentiation / astrocyte differentiation / positive regulation of cell adhesion mediated by integrin / lung alveolus development / regulation of cell differentiation / somatic stem cell population maintenance / decidualization / neuron development / maternal process involved in female pregnancy / blood vessel remodeling / animal organ regeneration / positive regulation of tyrosine phosphorylation of STAT protein / embryo implantation / negative regulation of angiogenesis / cytokine activity / stem cell differentiation / lung development / growth factor activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of neuron projection development / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / retina development in camera-type eye / positive regulation of peptidyl-serine phosphorylation / gene expression / fibroblast proliferation / cell population proliferation / positive regulation of MAPK cascade / response to hypoxia / immune response / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / cytosol
Similarity search - Function
Leukemia inhibitory factor / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Leukemia inhibitory factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRobinson, R.C. / Grey, L.M. / Staunton, D. / Stuart, D.I. / Heath, J.K. / Jones, E.Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1994
Title: The crystal structure and biological function of leukemia inhibitory factor: implications for receptor binding.
Authors: Robinson, R.C. / Grey, L.M. / Staunton, D. / Vankelecom, H. / Vernallis, A.B. / Moreau, J.F. / Stuart, D.I. / Heath, J.K. / Jones, E.Y.
History
DepositionDec 12, 1994-
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEUKEMIA INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)19,8911
Polymers19,8911
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.100, 56.200, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 17 / 2: CIS PROLINE - PRO 51

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Components

#1: Protein LEUKEMIA INHIBITORY FACTOR /


Mass: 19891.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P09056
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
210 mMMES1drop
340 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection% possible obs: 90 %
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.092

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→20 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 10610
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 50 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.92.9
X-RAY DIFFRACTIONx_mcangle_it4.34.3
X-RAY DIFFRACTIONx_scbond_it2.92.9
X-RAY DIFFRACTIONx_scangle_it4.34.3

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