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- PDB-5gw9: Crystal structure of C163, a backbone circularized G-CSF -

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Basic information

Entry
Database: PDB / ID: 5gw9
TitleCrystal structure of C163, a backbone circularized G-CSF
ComponentsGranulocyte colony-stimulating factor
KeywordsCYTOKINE / four-helix bundle / backbone circulatization
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMiyafusa, T. / Honda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science23510273 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.
Authors: Miyafusa, T. / Shibuya, R. / Honda, S.
History
DepositionSep 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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
D: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)70,3854
Polymers70,3854
Non-polymers00
Water8,611478
1
A: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)17,5961
Polymers17,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)17,5961
Polymers17,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)17,5961
Polymers17,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)17,5961
Polymers17,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Granulocyte colony-stimulating factor
C: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)35,1932
Polymers35,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area14360 Å2
MethodPISA
6
B: Granulocyte colony-stimulating factor

D: Granulocyte colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)35,1932
Polymers35,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area2000 Å2
ΔGint-18 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.941, 60.941, 178.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Granulocyte colony-stimulating factor / G-CSF / Pluripoietin


Mass: 17596.252 Da / Num. of mol.: 4 / Fragment: UNP residues 40-202 / Mutation: P40S, C47S, A205G
Source method: isolated from a genetically manipulated source
Details: 1st Ser and 173rd Gly 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


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.4M Ammonium sulfate

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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: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 89146 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 35.5
Reflection shellResolution: 1.65→1.693 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D9Q

2d9q


Resolution: 1.65→34.08 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.043 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21828 4463 5 %RANDOM
Rwork0.17733 ---
obs0.17939 84608 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å2-
2---0.09 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.65→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 0 478 5418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0195490
X-RAY DIFFRACTIONr_bond_other_d0.0030.025285
X-RAY DIFFRACTIONr_angle_refined_deg2.7191.9847516
X-RAY DIFFRACTIONr_angle_other_deg1.589312221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86524.587218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36215934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4591526
X-RAY DIFFRACTIONr_chiral_restr0.2170.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021256
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_it2.3892.1772847
X-RAY DIFFRACTIONr_mcbond_other2.3882.1772846
X-RAY DIFFRACTIONr_mcangle_it3.1493.2533641
X-RAY DIFFRACTIONr_mcangle_other3.1493.2533642
X-RAY DIFFRACTIONr_scbond_it3.9012.5572643
X-RAY DIFFRACTIONr_scbond_other3.92.5572644
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6573.73876
X-RAY DIFFRACTIONr_long_range_B_refined7.32819.0876900
X-RAY DIFFRACTIONr_long_range_B_other7.29518.5786723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 345 -
Rwork0.247 6255 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.28370.28140.20071.03320.78631.14410.04590.0362-0.01150.0811-0.01270.00240.12750.1309-0.03330.08240.037-0.03470.0484-0.01940.0459-0.635127.398-9.948
20.3384-0.3344-0.2071.08270.82551.16370.0434-0.0290.0145-0.0762-0.01320.0076-0.1330.1376-0.03020.0844-0.03870.03570.052-0.01890.0441-0.647118.90114.719
31.0946-0.158-0.75590.23960.16521.18430.04280.08140.00970.0377-0.01590.0142-0.1865-0.0486-0.02690.08690.0340.03070.04060.01970.0455-11.875146.868-15.029
41.12320.17020.78630.26940.23771.13160.0457-0.078-0.0067-0.0362-0.01290.01310.18-0.047-0.03280.0919-0.0328-0.03260.04150.0210.042518.595152.21519.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 173
2X-RAY DIFFRACTION2B11 - 173
3X-RAY DIFFRACTION3C11 - 173
4X-RAY DIFFRACTION4D11 - 173

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