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- PDB-5zo6: Crystal structure of C166, a backbone circularized G-CSF -

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Basic information

Entry
Database: PDB / ID: 5zo6
TitleCrystal structure of C166, a backbone circularized G-CSF
ComponentsGranulocyte colony-stimulating factor
KeywordsCYTOKINE / four-helix bundle / back-bone circularization
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 / Other interleukin signaling / positive regulation of actin filament polymerization / 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 / Other interleukin signaling / positive regulation of actin filament polymerization / 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 / response to ethanol / cellular response to lipopolysaccharide / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShibuya, R. / Miyafusa, T. / Honda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science23510273 Japan
CitationJournal: Febs J. / Year: 2019
Title: Stabilization of backbone-circularized protein is attained by synergistic gains in enthalpy of folded structure and entropy of unfolded structure.
Authors: Shibuya, R. / Miyafusa, T. / Honda, S.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
X: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)17,8941
Polymers17,8941
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9390 Å2
Unit cell
Length a, b, c (Å)47.180, 48.050, 54.960
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 / / G-CSF / Pluripoietin


Mass: 17893.605 Da / Num. of mol.: 1 / Fragment: UNP residues 37-205 / Mutation: C11S, A166G
Source method: isolated from a genetically manipulated source
Details: 166th Gly and 1st Ser are connected with a peptide bond
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF3, C17orf33, GCSF / Production host: Escherichia coli (E. coli) / References: UniProt: P09919
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 1.74 Å3/Da / Density % sol: 29.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: sodium acetate trihydrate, sodium chloride dehydrate, PEG 1500, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.15 Å / Num. obs: 14235 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 747 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BGC

1bgc


Resolution: 1.7→36.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.18 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21672 750 5.3 %RANDOM
Rwork0.16694 ---
obs0.16972 13466 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.11 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.7→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 105 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191302
X-RAY DIFFRACTIONr_bond_other_d0.0020.021264
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9911777
X-RAY DIFFRACTIONr_angle_other_deg1.04532919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53424.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54415218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.964155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4181.875670
X-RAY DIFFRACTIONr_mcbond_other2.4191.876669
X-RAY DIFFRACTIONr_mcangle_it4.0042.805839
X-RAY DIFFRACTIONr_mcangle_other4.0022.805840
X-RAY DIFFRACTIONr_scbond_it3.3262.198632
X-RAY DIFFRACTIONr_scbond_other3.3232.197633
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3243.175936
X-RAY DIFFRACTIONr_long_range_B_refined7.72114.8721541
X-RAY DIFFRACTIONr_long_range_B_other7.73514.7291510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 53 -
Rwork0.159 975 -
obs--99.42 %

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