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- PDB-3wo3: Crystal structure of IL-18 in complex with IL-18 receptor alpha -

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Basic information

Entry
Database: PDB / ID: 3wo3
TitleCrystal structure of IL-18 in complex with IL-18 receptor alpha
Components
  • Interleukin-18
  • Interleukin-18 receptor 1
KeywordsIMMUNE SYSTEM / binary complex / beta trefoil fold (ligand) / three immunoglobulin-like domains (receptor) / immunity / inflammation / autoimmunity / allergy / interleukin-18 receptor beta / glycosylation / serum / membrane
Function / homology
Function and homology information


interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation ...interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / neutrophil activation / negative regulation of myoblast differentiation / Interleukin-1 processing / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of NK T cell proliferation / Interleukin-37 signaling / sleep / positive regulation of macrophage derived foam cell differentiation / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / negative regulation of cold-induced thermogenesis / triglyceride homeostasis / T-helper 1 type immune response / positive regulation of tyrosine phosphorylation of STAT protein / natural killer cell mediated cytotoxicity / Interleukin-10 signaling / positive regulation of interleukin-17 production / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of smooth muscle cell proliferation / cholesterol homeostasis / cytokine activity / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / cell-cell signaling / signaling receptor activity / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / immune response / inflammatory response / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor type I/II / Interleukin-18 / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Interleukin-1 receptor type I/II / Interleukin-18 / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-18 receptor 1 / Interleukin-18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Kondo, N. / Shirakawa, M. / Kato, Z. / Tochio, H.
CitationJournal: Nat Commun / Year: 2014
Title: The structural basis for receptor recognition of human interleukin-18
Authors: Tsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Yamamoto, T. / Zuo, X. / Maenaka, K. / Park, E.Y. / Kondo, N. / Shirakawa, M. / Tochio, H. / Kato, Z.
History
DepositionDec 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 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: Interleukin-18
B: Interleukin-18 receptor 1
C: Interleukin-18
D: Interleukin-18 receptor 1
E: Interleukin-18
F: Interleukin-18 receptor 1
G: Interleukin-18
H: Interleukin-18 receptor 1
I: Interleukin-18
J: Interleukin-18 receptor 1
K: Interleukin-18
L: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,95984
Polymers324,83712
Non-polymers22,12272
Water1,78399
1
A: Interleukin-18
B: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,47916
Polymers54,1392
Non-polymers4,34014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-48 kcal/mol
Surface area23310 Å2
MethodPISA
2
C: Interleukin-18
D: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,69720
Polymers54,1392
Non-polymers4,55818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-73 kcal/mol
Surface area23500 Å2
MethodPISA
3
E: Interleukin-18
F: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,65316
Polymers54,1392
Non-polymers4,51414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-49 kcal/mol
Surface area23560 Å2
MethodPISA
4
G: Interleukin-18
H: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,90915
Polymers54,1392
Non-polymers3,76913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-94 kcal/mol
Surface area22280 Å2
MethodPISA
5
I: Interleukin-18
J: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7219
Polymers54,1392
Non-polymers2,5817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint1 kcal/mol
Surface area21950 Å2
MethodPISA
6
K: Interleukin-18
L: Interleukin-18 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5008
Polymers54,1392
Non-polymers2,3606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-12 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.490, 174.814, 183.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11L-506-

HOH

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Interleukin-18 / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 ...IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma


Mass: 18239.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14116
#2: Protein
Interleukin-18 receptor 1 / Interleukin-18 receptor alpha / IL-18R-1 / IL-18R1 / CD218 antigen-like family member A / CDw218a / ...Interleukin-18 receptor alpha / IL-18R-1 / IL-18R1 / CD218 antigen-like family member A / CDw218a / IL1 receptor-related protein / IL-1Rrp / IL1R-rp


Mass: 35899.738 Da / Num. of mol.: 6 / Fragment: UNP residues 20-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18R1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13478

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Sugars , 10 types, 34 molecules

#3: 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.: 3
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
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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.: 5
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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-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: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_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]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-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
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/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
#13: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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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Non-polymers , 2 types, 137 molecules

#12: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO4
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 50mM N-Cyclohexyl-3-aminopropanesulfonic acid, 35% pentaerythritol ethoxylate (15/4 EO/OH), 350mM ammonium sulfate, 50mM LysoFos Choline 10, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→43.93 Å / Num. all: 79498 / Num. obs: 79180 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 85.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.9
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F62

3f62


Resolution: 3.1→31.25 Å / Cor.coef. Fo:Fc: 0.9149 / Cor.coef. Fo:Fc free: 0.8855 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.355 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 3973 5.02 %RANDOM
Rwork0.1908 ---
obs0.1924 79095 99.43 %-
all-79548 --
Displacement parametersBiso max: 208.32 Å2 / Biso mean: 81.11 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-4.5079 Å20 Å20 Å2
2--2.4766 Å20 Å2
3----6.9844 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 3.1→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20507 0 1415 99 22021
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10790SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes573HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3148HARMONIC5
X-RAY DIFFRACTIONt_it22456HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3307SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23915SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d22456HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg30626HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2629 273 4.69 %
Rwork0.2268 5548 -
all0.2285 5821 -
obs--99.43 %
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)
15.5162-1.4076-1.25541.70830.36842.55030.0102-0.33470.59990.32540.1311-0.0449-0.2722-0.0724-0.1413-0.00390.05790.1599-0.28130.00990.1087-21.559877.4229-17.4068
200.33970.00930.54580.30220.5010.02090.1628-0.0502-0.116-0.02250.0191-0.02730.09090.0016-0.21360.1259-0.01720.06530.12520.029-2.560741.2512-41.3959
32.775-0.6572-0.46951.0328-0.24161.2754-0.0272-0.06460.17790.16640.15480.2013-0.0665-0.2582-0.1276-0.14640.0160.0936-0.26170.0386-0.0807-32.327869.9559-17.4113
45.7605-0.4883-0.7662.14890.63292.42250.14540.65170.679-0.17010.0052-0.1883-0.37040.1473-0.1506-0.2285-0.02870.0837-0.01580.08240.012815.016368.444-46.1821
53.7813-0.5303-0.441.02580.50670.81690.01590.39570.08520.05950.1255-0.1762-0.05930.2114-0.1414-0.27630.02190.00460.00990.0536-0.203318.930556.3123-47.269
64.7297-0.85011.39282.1223-0.92812.05460.13550.5189-0.6762-0.1514-0.03250.40620.2541-0.3418-0.103-0.26840.038-0.10060.0102-0.05460.1056-37.114428.7669-44.9909
74.4715-1.1419-0.02661.1662-0.23931.20520.00320.1161-0.1651-0.0216-0.00240.3071-0.0134-0.4338-0.0009-0.32960.097-0.0702-0.0105-0.0488-0.19-40.415340.5314-44.9911
84.3283-0.8317-0.27942.55010.22221.87580.09-0.0373-0.54650.1401-0.06140.06330.12310.1842-0.0286-0.09090.1586-0.0474-0.23390.05550.19181.857716.0911-23.3294
93.9932-0.95360.54241.63390.12611.52560.01530.1535-0.35880.0522-0.0152-0.19930.09610.3196-0.0001-0.24120.0402-0.0247-0.32290.1349-0.189411.743223.3449-22.6387
102.02961.53930.05435.7809-3.02153.25320.0612-0.19640.37270.25560.37570.8753-0.1498-0.7307-0.4369-0.38970.19890.15050.43260.304-0.2427-32.19093.6663-73.3294
111.89421.0889-0.68712.323-1.05160.85740.01540.08180.1134-0.15980.30220.6403-0.0497-0.4656-0.3176-0.15450.0981-0.03380.21250.1959-0.3985-27.773-7.6457-72.1281
123.58691.12720.52672.9661-1.0733.2806-0.14050.29310.32290.13820.43510.4407-0.9408-0.5768-0.29460.11380.14960.08530.16310.2955-0.3617-5.914432.1847-98.4295
131.37920.85710.02983.0006-1.22822.1491-0.22740.24790.13950.20970.2457-0.1756-0.5305-0.1514-0.0183-0.18-0.1388-0.06450.08620.1295-0.51794.623527.4058-101.089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|156}A1 - 156
2X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}A201 - 202
3X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}B820 - 824
4X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}C201 - 205
5X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}D419 - 425
6X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}E201 - 203
7X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}F821 - 825
8X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}G201 - 202
9X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}H817 - 821
10X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}I201
11X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}J401 - 413
12X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}K201
13X-RAY DIFFRACTION2{ A|201 - A|202 B|820 - B|824 C|201 - C|205 D|419 - D|425 E|201 - E|203 F|821 - F|825 G|201 - G|202 H|817 - H|821 I|201 - I|201 J|413 - J|413 K|201 - K|201 L|412 - L|412}L401 - 412
14X-RAY DIFFRACTION3{ B|-1 - B|315 B|901 - B|999}B-1 - 315
15X-RAY DIFFRACTION3{ B|-1 - B|315 B|901 - B|999}B901 - 999
16X-RAY DIFFRACTION4{ C|1 - C|156}C1 - 156
17X-RAY DIFFRACTION5{ D|-1 - D|316 D|902 - D|999}D-1 - 316
18X-RAY DIFFRACTION5{ D|-1 - D|316 D|902 - D|999}D902 - 999
19X-RAY DIFFRACTION6{ E|1 - E|157}E1 - 157
20X-RAY DIFFRACTION7{ F|-2 - F|316 F|901 - F|999}F-2 - 316
21X-RAY DIFFRACTION7{ F|-2 - F|316 F|901 - F|999}F901 - 999
22X-RAY DIFFRACTION8{ G|1 - G|156}G1 - 156
23X-RAY DIFFRACTION9{ H|-1 - H|316 H|901 - H|999}H-1 - 316
24X-RAY DIFFRACTION9{ H|-1 - H|316 H|901 - H|999}H901 - 999
25X-RAY DIFFRACTION10{ I|1 - I|156}I1 - 156
26X-RAY DIFFRACTION11{ J|21 - J|316 J|903 - J|999}J21 - 316
27X-RAY DIFFRACTION11{ J|21 - J|316 J|903 - J|999}J903 - 999
28X-RAY DIFFRACTION12{ K|1 - K|156}K1 - 156
29X-RAY DIFFRACTION13{ L|22 - L|315 L|905 - L|999}L22 - 315
30X-RAY DIFFRACTION13{ L|22 - L|315 L|905 - L|999}L905 - 999

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