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- PDB-1evs: CRYSTAL STRUCTURE OF HUMAN ONCOSTATIN M -

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Basic information

Entry
Database: PDB / ID: 1evs
TitleCRYSTAL STRUCTURE OF HUMAN ONCOSTATIN M
ComponentsONCOSTATIN M
KeywordsCYTOKINE / 4-helix bundle / gp130 binding cytokine
Function / homology
Function and homology information


oncostatin-M receptor binding / oncostatin-M-mediated signaling pathway / negative regulation of hormone secretion / positive regulation of acute inflammatory response / IL-6-type cytokine receptor ligand interactions / regulation of hematopoietic stem cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-17 production / positive regulation of cell division ...oncostatin-M receptor binding / oncostatin-M-mediated signaling pathway / negative regulation of hormone secretion / positive regulation of acute inflammatory response / IL-6-type cytokine receptor ligand interactions / regulation of hematopoietic stem cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-17 production / positive regulation of cell division / positive regulation of peptidyl-serine phosphorylation / cytokine activity / growth factor activity / positive regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / immune response / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Oncostatin-M / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsDeller, M.C. / Hudson, K.R. / Ikemizu, S. / Bravo, J. / Jones, E.Y. / Heath, J.K.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure and functional dissection of the cytostatic cytokine oncostatin M.
Authors: Deller, M.C. / Hudson, K.R. / Ikemizu, S. / Bravo, J. / Jones, E.Y. / Heath, J.K.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ONCOSTATIN M


Theoretical massNumber of molelcules
Total (without water)21,1431
Polymers21,1431
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.887, 53.285, 106.694
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 ONCOSTATIN M


Mass: 21143.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL TRUNCATION / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P13725
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 35000, ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1drop
3150 mM1dropNaCl
430 %(w/v)PEG350001reservoir
50.25 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 43901 / Num. obs: 10513 / % possible obs: 96.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.376 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 43901
Reflection shell
*PLUS
% possible obs: 98.2 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementResolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1082 -random
Rwork0.205 ---
all-10492 --
obs-9410 86.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 0 116 1435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0147
X-RAY DIFFRACTIONc_angle_deg1.7997
X-RAY DIFFRACTIONc_torsion_impr_deg1.0381
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8882
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.0381
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.336 / Num. reflection Rfree: 92 / % reflection Rfree: 8.6 % / Num. reflection Rwork: 870 / Rfactor obs: 0.271

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