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- PDB-2erj: Crystal structure of the heterotrimeric interleukin-2 receptor in... -

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Basic information

Entry
Database: PDB / ID: 2erj
TitleCrystal structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2
Components
  • (Interleukin-2 receptor ...) x 2
  • Cytokine receptor common gamma chain
  • Interleukin-2
KeywordsIMMUNE SYSTEM/CYTOKINE / INTERLEUKIN-2 / INTERLEUKIN-2 ALPHA RECEPTOR / INTERLEUKIN-2 BETA RECEPTOR / INTERLEUKIN-2 GAMMA RECEPTOR / IMMUNE SYSTEM-CYTOKINE COMPLEX
Function / homology
Function and homology information


regulation of T cell tolerance induction / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation ...regulation of T cell tolerance induction / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / positive regulation of T cell differentiation in thymus / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-7-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / leukocyte activation involved in immune response / interleukin-4-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / activated T cell proliferation / interleukin-15-mediated signaling pathway / kinase activator activity / positive regulation of regulatory T cell differentiation / cellular homeostasis / STAT3 nuclear events downstream of ALK signaling / natural killer cell activation / : / inflammatory response to antigenic stimulus / Interleukin-15 signaling / negative regulation of B cell apoptotic process / Interleukin-2 signaling / cytokine receptor activity / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / positive regulation of B cell differentiation / positive regulation of dendritic spine development / activation-induced cell death of T cells / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / cytokine binding / T cell differentiation / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / negative regulation of T cell proliferation / coreceptor activity / positive regulation of phagocytosis / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / Notch signaling pathway / Interleukin-7 signaling / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / gene expression / T cell differentiation in thymus / RAF/MAP kinase cascade / carbohydrate binding / positive regulation of cell growth / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / response to ethanol / adaptive immune response / transcription by RNA polymerase II / receptor complex / cell surface receptor signaling pathway / cell adhesion / endosome / inflammatory response / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / apoptotic process / cell surface / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site / : / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Complement Module, domain 1 / Complement Module; domain 1 / Growth Hormone; Chain: A; - #10 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / Rubrerythrin, domain 2 / Single Sheet / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha / Interleukin-2 receptor subunit beta / Cytokine receptor common subunit gamma / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDebler, E.W. / Stauber, D.J. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of the IL-2 signaling complex: Paradigm for a heterotrimeric cytokine receptor.
Authors: Stauber, D.J. / Debler, E.W. / Horton, P.A. / Smith, K.A. / Wilson, I.A.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 2.3Oct 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-2 receptor alpha chain
B: Interleukin-2 receptor beta chain
C: Cytokine receptor common gamma chain
D: Interleukin-2
E: Interleukin-2 receptor alpha chain
F: Interleukin-2 receptor beta chain
G: Cytokine receptor common gamma chain
H: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,16720
Polymers190,8578
Non-polymers5,31012
Water00
1
A: Interleukin-2 receptor alpha chain
B: Interleukin-2 receptor beta chain
C: Cytokine receptor common gamma chain
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,98210
Polymers95,4294
Non-polymers2,5536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Interleukin-2 receptor alpha chain
F: Interleukin-2 receptor beta chain
G: Cytokine receptor common gamma chain
H: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,18510
Polymers95,4294
Non-polymers2,7576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.266, 70.545, 129.236
Angle α, β, γ (deg.)83.85, 82.45, 89.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13B
23F
14C
24G
15C
25G
16D
26H
17A
27E
18B
28F
19A
29E

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUCYSCYSAA2 - 467 - 51
21LEULEUCYSCYSEE2 - 467 - 51
12SERSERGLNGLNBB6 - 2411 - 29
22SERSERGLNGLNFF6 - 2411 - 29
13ASNASNHISHISBB103 - 209108 - 214
23ASNASNHISHISFF103 - 209108 - 214
14LEULEUVALVALCC33 - 13038 - 135
24LEULEUVALVALGG33 - 13038 - 135
15ILEILESERSERCC131 - 226136 - 231
25ILEILESERSERGG131 - 226136 - 231
16THRTHRTHRTHRDD3 - 1333 - 133
26THRTHRTHRTHRHH3 - 1333 - 133
17SERSERSERSERAA54 - 6459 - 69
27SERSERSERSEREE54 - 6459 - 69
18THRTHRGLUGLUBB31 - 10236 - 107
28THRTHRGLUGLUFF31 - 10236 - 107
19LEULEUGLYGLYAA100 - 165105 - 170
29LEULEUGLYGLYEE100 - 165105 - 170

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
DetailsThis entry contains the crystallographic asymmetric unit wich consists of two biological assemblies: ABCD and EFGH.

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Components

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Interleukin-2 receptor ... , 2 types, 4 molecules AEBF

#1: Protein Interleukin-2 receptor alpha chain / IL-2 RECEPTOR ALPHA SUBUNIT, p55, CD25, TAC ANTIGEN / IL-2 receptor alpha subunit / IL-2-RA / IL2-RA / p55 / CD25 / TAC antigen


Mass: 25402.438 Da / Num. of mol.: 2 / Mutation: N49S,N68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01589
#2: Protein Interleukin-2 receptor beta chain / IL-2 RECEPTOR BETA SUBUNIT, p75, CD122 / IL-2 receptor beta subunit / IL-2-RB / p75 / CD122


Mass: 25452.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14784

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Protein , 2 types, 4 molecules CGDH

#3: Protein Cytokine receptor common gamma chain / INTERLEUKIN-2 RECEPTOR GAMMA CHAIN, IL-2 RECEPTOR GAMMA SUBUNIT, p65, CD132 / IL-2 receptor Gamma subunit / IL-2-RG / p65 / CD132


Mass: 29169.512 Da / Num. of mol.: 2 / Mutation: N58Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P31785
#4: Protein Interleukin-2 / IL-2 / T-cell growth factor / TCGF / Aldesleukin


Mass: 15403.915 Da / Num. of mol.: 2 / Mutation: C125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60568

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Sugars , 6 types, 12 molecules

#5: 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.: 2
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
#6: 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
#7: 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.: 2
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
#8: 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
#9: 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
#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.: 4
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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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: MPEG 550, sodium acetate, sodium citrate, phenol, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3→129.1 Å / Num. all: 39459 / Num. obs: 37249 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rsym value: 0.08 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 3924 / Rsym value: 0.5 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB structure 2B5I

2b5i


Resolution: 3→129.1 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 44.957 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26288 1864 5 %RANDOM
Rwork0.22047 ---
all0.22254 37863 --
obs0.22254 35379 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-1.12 Å2-0.81 Å2
2--0.29 Å2-0.37 Å2
3---0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.682 Å
Refinement stepCycle: LAST / Resolution: 3→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10837 0 350 0 11187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111533
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.96915716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44651307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88823.96553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.496151914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5131572
X-RAY DIFFRACTIONr_chiral_restr0.0830.21750
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028580
X-RAY DIFFRACTIONr_nbd_refined0.2170.24111
X-RAY DIFFRACTIONr_nbtor_refined0.3120.27626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.28
X-RAY DIFFRACTIONr_mcbond_it0.341.56755
X-RAY DIFFRACTIONr_mcangle_it0.622210767
X-RAY DIFFRACTIONr_scbond_it0.9335420
X-RAY DIFFRACTIONr_scangle_it1.6594.54949
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A354loose positional0.315
2B156loose positional0.135
3B890loose positional0.245
4C820loose positional0.365
5C833loose positional0.265
6D1069loose positional0.255
7A85loose positional0.475
8B584loose positional0.555
9A532loose positional0.415
1A354loose thermal1.0110
2B156loose thermal1.2210
3B890loose thermal1.0910
4C820loose thermal1.1210
5C833loose thermal1.0610
6D1069loose thermal0.8810
7A85loose thermal0.5710
8B584loose thermal1.7510
9A532loose thermal1.0210
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 92 -
Rwork0.314 1714 -
obs--62.53 %
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)
18.6348-5.59342.47038.1623-3.12352.1264-0.012-0.60980.074-0.0273-0.098-0.4711-0.19990.11220.110.1629-0.11370.0675-0.31810.00120.031223.559851.4258-11.579
25.8648-0.45781.68267.6066-0.18247.43610.0771-1.38560.04481.0133-0.1983-0.6425-0.2970.34130.1213-0.56130.0437-0.1250.0507-0.0797-0.176733.375918.909228.8567
312.40251.242-3.19033.49010.15843.4012-0.1609-0.9736-0.6290.04840.09030.25380.1534-0.27520.0707-0.60560.203-0.1522-0.17470.0351-0.5445.00158.443922.4966
44.92620.57033.38575.4531-0.833714.1727-0.26771.21510.8759-1.02680.0724-0.0849-0.88960.14370.1952-0.0105-0.078-0.0059-0.3660.1107-0.33714.549112.2498-27.5895
57.16780.6039-5.54256.7253-2.283812.6204-0.4069-0.3856-0.6074-0.01040.24720.49670.9591-0.72620.1597-0.40610.0116-0.1178-0.45640.0476-0.39763.6827-0.00753.1795
68.2249-0.46851.08410.9421-1.675710.9324-0.1559-0.34250.518-0.20830.2996-0.1366-0.3807-0.0013-0.1437-0.5254-0.0179-0.0531-0.5437-0.0663-0.355327.296723.3276-2.5055
77.13275.6029-0.88257.4776-1.7572.9643-0.080.23920.3181-0.0112-0.25730.36240.1069-0.12210.33740.1960.0218-0.2041-0.1956-0.13340.00484.403510.797371.0423
88.6932-0.5656-3.09697.13022.71066.11930.13750.9307-0.1299-0.5473-0.0531-0.5467-0.00220.3662-0.0845-0.66010.0766-0.1442-0.2985-0.1368-0.26715.212841.319631.8956
914.2801-0.32843.17373.62750.33473.76220.23420.59620.5155-0.0944-0.13530.2606-0.1875-0.2458-0.099-0.5465-0.0225-0.0049-0.485-0.0045-0.592-13.087452.16736.5488
104.1751-0.7898-2.8326.9193-2.65136.5222-0.0069-1.9484-0.63671.5120.07170.4530.3961-0.1554-0.06480.3562-0.32040.03980.6794-0.0106-0.216-6.101150.370786.1404
118.3429-0.475.02214.9176-1.599512.09050.0046-0.20890.69850.1396-0.13560.3227-0.5172-0.66220.131-0.4351-0.08640.0773-0.4266-0.1945-0.3369-14.604262.049354.9592
126.8461-0.1223-0.317310.084-1.176910.78780.1340.116-0.38280.38130.0062-0.06490.194-0.1837-0.1402-0.3634-0.0956-0.1671-0.34930.0139-0.36588.497938.535262.4605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1656 - 170
2X-RAY DIFFRACTION2BB6 - 10211 - 107
3X-RAY DIFFRACTION3BB103 - 209108 - 214
4X-RAY DIFFRACTION4CC32 - 13037 - 135
5X-RAY DIFFRACTION5CC131 - 226136 - 231
6X-RAY DIFFRACTION6DD3 - 1333 - 133
7X-RAY DIFFRACTION7EE1 - 1656 - 170
8X-RAY DIFFRACTION8FF6 - 10211 - 107
9X-RAY DIFFRACTION9FF103 - 209108 - 214
10X-RAY DIFFRACTION10GG32 - 13037 - 135
11X-RAY DIFFRACTION11GG131 - 226136 - 231
12X-RAY DIFFRACTION12HH3 - 1333 - 133

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