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- PDB-1ykb: Crystal Structure of Insect Cell Expressed IL-22 -

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Basic information

Entry
Database: PDB / ID: 1ykb
TitleCrystal Structure of Insect Cell Expressed IL-22
ComponentsPROTEIN (Interleukin-22)
KeywordsCYTOKINE / interleukin / il-22 / glycosylation
Function / homology
Function and homology information


interleukin-22 receptor binding / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / inflammatory response / extracellular space / extracellular region
Similarity search - Function
Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXu, T. / Logsdon, N.J. / Walter, M.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of insect-cell-derived IL-22.
Authors: Xu, T. / Logsdon, N.J. / Walter, M.R.
History
DepositionJan 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Interleukin-22)
B: PROTEIN (Interleukin-22)
C: PROTEIN (Interleukin-22)
D: PROTEIN (Interleukin-22)
E: PROTEIN (Interleukin-22)
F: PROTEIN (Interleukin-22)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,24415
Polymers98,4176
Non-polymers3,8279
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.877, 62.227, 139.524
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Non-polymers , 2 types, 57 molecules ABCDEF

#1: Protein
PROTEIN (Interleukin-22) / IL-22 / IL-10-related T-cell-derived inducible factor / IL-TIF / UNQ3099/PRO10096


Mass: 16402.914 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22, ILTIF / References: UniProt: Q9GZX6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 9 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.86 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.255 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.255 Å / Relative weight: 1
ReflectionResolution: 2.5→42.95 Å / Num. all: 35584 / Num. obs: 33239 / Observed criterion σ(F): 0 / Biso Wilson estimate: 46.9 Å2 / Limit h max: 23 / Limit h min: -24 / Limit k max: 24 / Limit k min: -24 / Limit l max: 55 / Limit l min: 0 / Observed criterion F max: 1022737.25 / Observed criterion F min: 8.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.93 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1651 5 %Random
Rwork0.232 ---
all-34487 --
obs-32762 95 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 34.1109 Å2 / ksol: 0.304824 e/Å3
Displacement parametersBiso max: 123.17 Å2 / Biso mean: 60.32 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-6.52 Å20 Å2-0.52 Å2
2---1.18 Å20 Å2
3----5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 252 51 7179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg19.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.96
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.3841755.10.35332570.0294267343280.4
2.72-2.860.3571804.60.33137440.0274252392492.3
2.86-3.040.3622125.10.31239150.0254292412796.2
3.04-3.270.3112205.20.25539790.0214326419997.1
3.27-3.60.26420850.23939690.0184297417797.2
3.6-4.120.2532054.80.2140330.0184315423898.2
4.12-5.170.2272415.60.19440580.0154325429999.4
5.17-19.930.2372104.80.21341560.0164433436698.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.param

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