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- PDB-1rhg: THE STRUCTURE OF GRANULOCYTE-COLONY-STIMULATING FACTOR AND ITS RE... -

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Basic information

Entry
Database: PDB / ID: 1rhg
TitleTHE STRUCTURE OF GRANULOCYTE-COLONY-STIMULATING FACTOR AND ITS RELATIONSHIP TO THOSE OF OTHER GROWTH FACTORS
ComponentsGRANULOCYTE COLONY-STIMULATING FACTOR
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


granulocyte colony-stimulating factor receptor binding / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / regulation of actin filament organization / positive regulation of actin filament polymerization / Other interleukin signaling / cellular response to cytokine stimulus / Interleukin-10 signaling / Signaling by CSF3 (G-CSF) ...granulocyte colony-stimulating factor receptor binding / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / regulation of actin filament organization / positive regulation of actin filament polymerization / Other interleukin signaling / cellular response to cytokine stimulus / Interleukin-10 signaling / Signaling by CSF3 (G-CSF) / endocytic vesicle lumen / lysosomal lumen / cytokine activity / growth factor activity / Inactivation of CSF3 (G-CSF) signaling / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to lipopolysaccharide / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / positive regulation of cell population proliferation / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
GCSF/MGF / Granulocyte colony-stimulating factor / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Granulocyte colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHill, C.P. / Osslund, T.D. / Eisenberg, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors.
Authors: Hill, C.P. / Osslund, T.D. / Eisenberg, D.
#1: Journal: To be Published
Title: Towards Automated Crystallization
Authors: Osslund, T.D. / Luthy, R. / Cascio, D. / Eisenberg, D.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Folding and Oxidation of Recombinant Human Granulocyte Colony Stimulating Factor Produced in Escherichia Coli. Characterization of the Disulfide-Reduced Intermediates and Cysteine-Serine Analogs
Authors: Lu, H.S. / Clogston, C.L. / Narhi, L.O. / Merewether, L.A. / Pearl, W.R. / Boone, T.C.
#3: Journal: Science / Year: 1986
Title: Recombinant Human Granulocyte Colony-Stimulating Factor: Effects on Normal and Leukemic Myeloid Cells
Authors: Souza, L.M. / Boone, T.C. / Gabrilove, J. / Lai, P.H. / Zsebo, K.M. / Murdock, D.C. / Chazin, V.R. / Bruszewski, J. / Lu, H. / Chen, K.C. / Barendt, J. / Platzer, E. / Moore, M.A.S. / Mertelsmann, R. / Welte, K.
History
DepositionJan 29, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRANULOCYTE COLONY-STIMULATING FACTOR
B: GRANULOCYTE COLONY-STIMULATING FACTOR
C: GRANULOCYTE COLONY-STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)56,0573
Polymers56,0573
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.900, 110.700, 49.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.837465, 0.162405, 0.521802), (-0.294485, -0.670224, 0.681233), (0.46036, -0.724171, -0.513463)0.389, 83.496, 8.978
2given(-0.763481, 0.140255, 0.630416), (0.120204, -0.928217, 0.352085), (0.634545, 0.344589, 0.691817)69.62, 101.215, -46.857
3given(-0.382797, 0.549495, 0.742645), (-0.664126, 0.395119, -0.634679), (-0.642186, -0.736163, 0.213684)27.059, 39.814, 76.862

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Components

#1: Protein GRANULOCYTE COLONY-STIMULATING FACTOR


Mass: 18685.564 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09919
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal grow
*PLUS
pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %(w/v)PEG80001reservoir
2380 mM1reservoirMgSO4
3220 mM1reservoirLiCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 10735 / % possible obs: 93.3 % / Num. measured all: 50868 / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.215 / Rfactor obs: 0.215 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 0 120 4114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.354
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rfactor obs: 0.215 / Rfactor Rfree: 0.344
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.354
X-RAY DIFFRACTIONx_dihedral_angle_d20.805
X-RAY DIFFRACTIONx_improper_angle_d1.437
X-RAY DIFFRACTIONx_mcbond_it1.63

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