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- PDB-4o6k: The crystal structure of zebrafish IL-22 -

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Basic information

Entry
Database: PDB / ID: 4o6k
TitleThe crystal structure of zebrafish IL-22
ComponentsInterleukin 22
KeywordsIMMUNE SYSTEM / IL-22 / interleukin-22 / zIL-22
Function / homologyGrowth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / regulation of inflammatory response / defense response to Gram-negative bacterium / immune response / Up-down Bundle / Mainly Alpha / Interleukin-22
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSiupka, P. / Hamming, O.J. / Fretaud, M. / Luftalla, G. / Levraud, J.P. / Hartmann, R.
CitationJournal: Genes Immun. / Year: 2014
Title: The crystal structure of zebrafish IL-22 reveals an evolutionary, conserved structure highly similar to that of human IL-22.
Authors: Siupka, P. / Hamming, O.J. / Fretaud, M. / Luftalla, G. / Levraud, J.P. / Hartmann, R.
History
DepositionDec 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Other
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 22
B: Interleukin 22
C: Interleukin 22
D: Interleukin 22


Theoretical massNumber of molelcules
Total (without water)66,8834
Polymers66,8834
Non-polymers00
Water4,486249
1
A: Interleukin 22


Theoretical massNumber of molelcules
Total (without water)16,7211
Polymers16,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interleukin 22


Theoretical massNumber of molelcules
Total (without water)16,7211
Polymers16,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Interleukin 22


Theoretical massNumber of molelcules
Total (without water)16,7211
Polymers16,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Interleukin 22


Theoretical massNumber of molelcules
Total (without water)16,7211
Polymers16,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.940, 50.440, 65.800
Angle α, β, γ (deg.)72.04, 85.94, 62.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Interleukin 22 / Uncharacterized protein


Mass: 16720.689 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 71-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: il22, IL-22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.95 Å3/Da / Density % sol: 37.01 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→27.761 Å / Num. all: 29505 / Num. obs: 29004 / % possible obs: 98.3 %

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.761 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 2002 6.9 %
Rwork0.2223 --
obs0.2239 29004 98.3 %
all-29505 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→27.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 0 249 4641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114546
X-RAY DIFFRACTIONf_angle_d1.2466140
X-RAY DIFFRACTIONf_dihedral_angle_d15.8641701
X-RAY DIFFRACTIONf_chiral_restr0.092659
X-RAY DIFFRACTIONf_plane_restr0.007800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1002-2.15270.25671430.247185097
2.1527-2.21080.25361440.2443194698
2.2108-2.27590.26891410.2345192198
2.2759-2.34930.25731470.2363191798
2.3493-2.43320.26471450.2276192498
2.4332-2.53060.26651480.2342195498
2.5306-2.64570.28531370.2366191898
2.6457-2.7850.26361450.2302195998
2.785-2.95930.21541360.2347192599
2.9593-3.18750.27351470.2232191399
3.1875-3.50770.24861460.2164192799
3.5077-4.0140.20961420.2102195599
4.014-5.05220.22871430.1902196599
5.0522-27.76350.24491380.2314192898

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