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- PDB-3wo4: Crystal structure of the IL-18 signaling ternary complex -

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Basic information

Entry
Database: PDB / ID: 3wo4
TitleCrystal structure of the IL-18 signaling ternary complex
Components
  • (Interleukin-18 receptor ...) x 2
  • Interleukin-18
KeywordsIMMUNE SYSTEM / ternary complex / beta trefoil fold (ligand) / three immunoglobulin-like domains (receptors) / immunity / inflammation / autoimmunity / allergy / 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 natural killer cell mediated cytotoxicity / 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 / coreceptor activity / 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 / cellular response to hydrogen peroxide / 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 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Immunoglobulin domain ...Interleukin-1 receptor type I/II / Interleukin-18 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Immunoglobulin domain / 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 accessory protein / 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 / 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 / _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 2.2Nov 20, 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 receptor accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,47214
Polymers93,3753
Non-polymers5,09711
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint49 kcal/mol
Surface area40240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.560, 111.560, 134.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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

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Interleukin-18 receptor ... , 2 types, 2 molecules BC

#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.: 1 / 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
#3: Protein Interleukin-18 receptor accessory protein / Interleukin-18 receptor beta / IL-18 receptor accessory protein / IL-18RAcP / Accessory protein- ...Interleukin-18 receptor beta / IL-18 receptor accessory protein / IL-18RAcP / Accessory protein-like / AcPL / CD218 antigen-like family member B / CDw218b / IL-1R accessory protein-like / IL-1RAcPL / Interleukin-1 receptor 7 / IL-1R-7 / IL-1R7 / Interleukin-18 receptor accessory protein-like / IL-18R-beta / IL-18Rbeta


Mass: 39235.637 Da / Num. of mol.: 1 / Fragment: UNP residues 15-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18RAP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95256

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Sugars , 7 types, 10 molecules

#4: 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
#5: 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.: 1
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
#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.: 1
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 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.: 2
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
#8: 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.: 1
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
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 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.: 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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Non-polymers , 2 types, 32 molecules

#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM Tris-HCl, 18% polyethylene glycol 4000, 200mM magnesium chloride, 40mM hexaamminecobalt (III) chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 20680 / Num. obs: 20659 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 60.09 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 19.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2029 / % possible all: 99.3

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Processing

Software
NameVersionClassification
UGUISdata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WO3

3wo3


Resolution: 3.1→42 Å / Cor.coef. Fo:Fc: 0.9234 / Cor.coef. Fo:Fc free: 0.8813 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 881 5.07 %RANDOM
Rwork0.1876 ---
obs0.1899 17368 84.97 %-
all-20440 --
Displacement parametersBiso max: 188.95 Å2 / Biso mean: 77.81 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1--4.8362 Å20 Å20 Å2
2--3.7787 Å20 Å2
3---1.0575 Å2
Refine analyzeLuzzati coordinate error obs: 0.616 Å
Refinement stepCycle: LAST / Resolution: 3.1→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 336 31 6024
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2892SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes870HARMONIC5
X-RAY DIFFRACTIONt_it6145HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion917SEMIHARMONIC5
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_contact6581SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6145HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8391HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion3.67
LS refinement shellResolution: 3.1→3.29 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2974 86 4.71 %
Rwork0.2089 1739 -
all0.2132 1825 -
obs--84.97 %
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)
10.30590.0055-0.49794.9527-0.54326.8836-0.10170.10280.0139-0.0243-0.0305-0.03030.06050.13270.13220.0385-0.03990.1019-0.1714-0.0219-0.217-26.1456-15.09448.6082
20.9713-0.3396-0.83231.81530.75984.14210.04380.2777-0.0169-0.2806-0.19740.2834-0.0375-0.58590.1536-0.0485-0.0933-0.0693-0.32590.0165-0.3156-32.4379-8.56490.4087
31.3142-0.3077-0.68012.02510.27621.2374-0.0415-0.06650.11570.06380.0241-0.3605-0.38020.16920.01740.1224-0.09340.0193-0.31390.0208-0.1913-17.543418.79520.9466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 157
2X-RAY DIFFRACTION2{ B|* }B-2 - 318
3X-RAY DIFFRACTION3{ C|* }C30 - 356

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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