5GW9

Crystal structure of C163, a backbone circularized G-CSF

> Summary

Summary for 5GW9

DescriptorGranulocyte colony-stimulating factor (2 entities in total)
Functional Keywordscytokine, four-helix bundle, backbone circulatization
Biological sourceHomo sapiens (Human)
Cellular locationSecreted P09919
Total number of polymer chains4
Total molecular weight70385.01
Authors
Miyafusa, T.,Honda, S. (deposition date: 2016-09-09, release date: 2017-09-13)
Primary citation
Miyafusa, T.,Honda, S.
Crystal structure of C163, a backbone circularized G-CSF
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.65 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.22890.5%4.9%3.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gw9
no rotation
Molmil generated image of 5gw9
rotated about x axis by 90°
Molmil generated image of 5gw9
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5gw9
no rotation
Molmil generated image of 5gw9
rotated about x axis by 90°
Molmil generated image of 5gw9
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5gw9.pdb1.gz [58.18 KB])
Coordinate files for Biological unit (5gw9.pdb2.gz [58.1 KB])
Coordinate files for Biological unit (5gw9.pdb3.gz [58.53 KB])
Coordinate files for Biological unit (5gw9.pdb4.gz [57.59 KB])
Coordinate files for Biological unit (5gw9.pdb5.gz [114.78 KB])
Coordinate files for Biological unit (5gw9.pdb6.gz [113.98 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, DGranulocyte colony-stimulating factorpolymer16317596.34
UniProt (P09919)
Homo sapiens (Human)G-CSF,Pluripoietin
waterwater18.0478

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight70385.0
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight70385.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.65 Å)

Cell axes60.94160.941178.509
Cell angles90.0090.00120.00
SpacegroupP 32
Resolution limits34.08 - 1.65
the highest resolution shell value1.693 - 1.650
R-factor0.17939
R-work0.17733
the highest resolution shell value0.247
R-free0.21828
the highest resolution shell value0.277
RMSD bond length0.034
RMSD bond angle2.719

Data Collection Statistics

Resolution limits50.00 - 1.65
the highest resolution shell value -
Number of reflections89146
Rmerge_l_obs0.062
the highest resolution shell value0.640
Completeness99.9
Redundancy5.7
the highest resolution shell value5.6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1EVAPORATION293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5gw9.ent.gz (233.15 KB)
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all (no-compress)pdb5gw9.ent (935.85 KB)
header onlypdb5gw9.ent.gz (7.75 KB)
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PDBx/mmCIF5gw9.cif.gz (274.5 KB)
PDBMLall5gw9.xml.gz (376.22 KB)
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no-atom5gw9-noatom.xml.gz (28.58 KB)
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ext-atom5gw9-extatom.xml.gz (130.9 KB)
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PDBMLplusall5gw9-plus.xml.gz (376.93 KB)
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no-atom5gw9-plus-noatom.xml.gz (29.29 KB)
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add only5gw9-add.xml.gz (725 B)
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RDF5gw9.rdf.gz (57.54 KB)
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Structure factorsr5gw9sf.ent.gz (1.84 MB)
Biological unit (PDB format)5gw9.pdb1.gz (58.18 KB) (A)
*author defined assembly, 1 molecule(s) (monomeric)
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5gw9.pdb2.gz (58.1 KB) (B)
*author defined assembly, 1 molecule(s) (monomeric)
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5gw9.pdb3.gz (58.53 KB) (C)
*author defined assembly, 1 molecule(s) (monomeric)
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5gw9.pdb4.gz (57.59 KB) (D)
*author defined assembly, 1 molecule(s) (monomeric)
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5gw9.pdb5.gz (114.78 KB) (A,C)
*software defined assembly, 2 molecule(s) (dimeric)
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5gw9.pdb6.gz (113.98 KB) (B)
*software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5gw9​_validation.pdf.gz (277.89 KB)
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PDF-full5gw9​_full​_validation.pdf.gz (303.41 KB)
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XML5gw9​_validation.xml.gz (32.16 KB)
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PNG5gw9​_multipercentile​_validation.png.gz (158.82 KB)
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SVG5gw9​_multipercentile​_validation.svg.gz (944 B)
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Sequence (fasta)5gw9​_seq.txt
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