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- PDB-1bgc: CRYSTAL STRUCTURE OF CANINE AND BOVINE GRANULOCYTE-COLONY STIMULA... -

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Basic information

Entry
Database: PDB / ID: 1bgc
TitleCRYSTAL STRUCTURE OF CANINE AND BOVINE GRANULOCYTE-COLONY STIMULATING FACTOR (G-CSF)
ComponentsGRANULOCYTE COLONY-STIMULATING FACTOR
KeywordsCYTOKINE
Function / homology
Function and homology information


Other interleukin signaling / Signaling by CSF3 (G-CSF) / positive regulation of biosynthetic process / granulocyte colony-stimulating factor receptor binding / positive regulation of myeloid cell differentiation / Inactivation of CSF3 (G-CSF) signaling / cytokine activity / growth factor activity / immune response / positive regulation of cell population proliferation / extracellular space
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsLovejoy, B. / Cascio, D. / Eisenberg, D.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of canine and bovine granulocyte-colony stimulating factor (G-CSF).
Authors: Lovejoy, B. / Cascio, D. / Eisenberg, D.
History
DepositionApr 27, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANULOCYTE COLONY-STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)18,9721
Polymers18,9721
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.000, 53.900, 57.100
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 GRANULOCYTE COLONY-STIMULATING FACTOR


Mass: 18971.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P35833
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.86 Å3/Da / Density % sol: 34.03 %
Crystal grow
*PLUS
pH: 3.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlbovine G-CSF solution1drop
250 mMMES1dropadjusted to pH5.5 with NaOH
350 mMMES1reservoiradjusted to pH5.5 with NaOH

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 15100 / % possible obs: 93 % / Observed criterion σ(F): 1 / Num. measured all: 74290 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→7 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.213 -
obs0.213 14989
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 0 291 1742
Refine LS restraints
Refine-IDTypeDev ideal
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_deg2.59
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
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 7 Å / Num. reflection obs: 14989 / σ(F): 1 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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