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

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Basic information

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


granulocyte colony-stimulating factor receptor binding / positive regulation of myeloid cell differentiation / 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 speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 1.4Oct 23, 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)18,8721
Polymers18,8721
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.200, 36.200, 48.600
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE 129 IS A CIS PROLINE.

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Components

#1: Protein GRANULOCYTE COLONY-STIMULATING FACTOR


Mass: 18871.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / References: UniProt: P35834
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.54
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122.8 mg/mlcanine G-CSF solution1drop
25.80 %(v/v)ethanol1drop
350 mMHEPES1dropadjusted to pH6.54 with NaOH
4200 mMammonium sulfate1drop
55.80 %(v/v)ethanol1reservoir
650 mMHEPES1reservoiradjusted to pH6.54 with NaOH
7200 mMammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 6830 / % possible obs: 88.2 % / Num. measured all: 18417 / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→7 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.207 -
obs0.207 6532
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 0 174 1587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.57
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: 2.3 Å / Lowest resolution: 7 Å / Num. reflection obs: 6532 / σ(F): 1 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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