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- PDB-5ijc: The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex -

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Basic information

Entry
Database: PDB / ID: 5ijc
TitleThe crystal structure of mouse TLR4/MD-2/neoseptin-3 complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4,Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Immune response / protein complex / small molecule agonist
Function / homology
Function and homology information


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / innate immune response-activating signaling pathway / regulation of dendritic cell cytokine production / positive regulation of lymphocyte proliferation / detection of lipopolysaccharide / mast cell activation / intestinal epithelial structure maintenance / negative regulation of interleukin-23 production / lymphocyte proliferation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / leukotriene metabolic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / response to fatty acid / activation of NF-kappaB-inducing kinase activity / regulation of tumor necrosis factor production / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage cytokine production / negative regulation of cold-induced thermogenesis / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor 4 signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / B cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / phosphatidylinositol 3-kinase binding / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / neurogenesis / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to bacterium / microglial cell activation / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / ML domain / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / ML domain / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
neoseptin 3 / Variable lymphocyte receptor B / Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. ...Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.
Authors: Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M.M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K.W. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 27, 2016ID: 5HG4
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Jul 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / citation / computing / database_PDB_caveat / diffrn / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.angle_beta / _cell.volume ..._cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _struct.pdbx_CASP_flag / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _symmetry.space_group_name_Hall
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 3.1Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 4,Variable lymphocyte receptor B
C: Lymphocyte antigen 96
B: Toll-like receptor 4,Variable lymphocyte receptor B
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,27724
Polymers186,8234
Non-polymers6,45420
Water3,837213
1
A: Toll-like receptor 4,Variable lymphocyte receptor B
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,53712
Polymers93,4122
Non-polymers3,12510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint20 kcal/mol
Surface area33330 Å2
MethodPISA
2
C: Lymphocyte antigen 96
B: Toll-like receptor 4,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74012
Polymers93,4122
Non-polymers3,32810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint19 kcal/mol
Surface area33790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.752, 148.559, 131.720
Angle α, β, γ (deg.)90.000, 98.304, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 4,Variable lymphocyte receptor B


Mass: 71649.758 Da / Num. of mol.: 2
Fragment: TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr4, Lps, VLRB / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9QUK6, UniProt: Q4G1L2, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 21761.857 Da / Num. of mol.: 2 / Fragment: UNP residues 19-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly96, Esop1, Md2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JHF9

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Sugars , 2 types, 16 molecules

#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.: 5 / Source method: isolated from a natural 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
#4: 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.: 11 / Source method: isolated from a natural 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, 217 molecules

#5: Chemical
ChemComp-V2A / neoseptin 3 / tert-butyl (2S)-2-({4-amino-3-[2-(4-hydroxyphenyl)ethyl]benzene-1-carbonyl}amino)-4-phenylbutanoate


Mass: 474.591 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C29H34N2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 84084 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.67 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.116 / Χ2: 0.88 / Net I/σ(I): 7.2 / Num. measured all: 315421
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.55-2.593.30.95940860.5580.6060.7197.5
2.59-2.643.40.85841600.7130.5340.73698.7
2.64-2.693.60.77541790.6650.4770.7899.50.914
2.69-2.753.70.62742000.7350.380.78499.90.736
2.75-2.813.80.56942170.8020.340.80599.90.665
2.81-2.873.80.46541710.850.2780.78999.90.544
2.87-2.943.90.38942020.8840.2320.83499.80.455
2.94-3.023.90.33142530.9140.1970.84699.90.386
3.02-3.113.80.25141840.9510.150.8711000.293
3.11-3.213.90.20541830.960.1220.95799.90.239
3.21-3.333.90.16742390.9730.0990.9899.90.194
3.33-3.463.90.13542150.9770.0811.06999.90.158
3.46-3.623.80.11342140.980.0681.10999.90.132
3.62-3.813.80.09441690.9850.0561.10599.90.11
3.81-4.053.80.08142450.9870.0491.04199.90.095
4.05-4.363.80.07442060.9890.0450.96799.80.087
4.36-4.83.80.06942330.9890.0420.90299.90.081
4.8-5.493.80.06742100.9880.0410.83499.80.079
5.49-6.923.70.06442630.9860.0390.73399.80.075
6.92-503.70.05642550.9910.0350.65898.60.066

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IJB

5ijb


Resolution: 2.57→42.36 Å / SU ML: 0.2922 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.8528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2000 2.74 %RANDOM
Rwork0.1934 71117 --
obs0.1946 73117 85.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.48 Å2
Refinement stepCycle: LAST / Resolution: 2.57→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11617 0 434 215 12266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002512337
X-RAY DIFFRACTIONf_angle_d0.594616712
X-RAY DIFFRACTIONf_chiral_restr0.05561939
X-RAY DIFFRACTIONf_plane_restr0.00332102
X-RAY DIFFRACTIONf_dihedral_angle_d13.27737335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.630.3616600.28762139X-RAY DIFFRACTION36.01
2.63-2.70.3327850.26733030X-RAY DIFFRACTION50.98
2.7-2.780.25811050.24123705X-RAY DIFFRACTION62.86
2.78-2.870.29951220.24084369X-RAY DIFFRACTION73.27
2.87-2.980.29021380.23874884X-RAY DIFFRACTION82.21
2.98-3.10.31791530.24655475X-RAY DIFFRACTION92.28
3.1-3.240.30791660.245893X-RAY DIFFRACTION99.04
3.24-3.410.24461670.2195907X-RAY DIFFRACTION99.82
3.41-3.620.26671660.18965922X-RAY DIFFRACTION99.89
3.62-3.90.19911680.17235961X-RAY DIFFRACTION99.82
3.9-4.290.17081670.15085927X-RAY DIFFRACTION99.82
4.29-4.910.19071670.13985954X-RAY DIFFRACTION99.8
4.91-6.190.2011680.17495980X-RAY DIFFRACTION99.77
6.19-42.360.22921680.20565971X-RAY DIFFRACTION98.49
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)
12.35903705888-0.392321694343-1.374317312260.977406751470.7087005238571.995574229720.0340596216012-0.416743486313-0.8186794380070.2667851000040.0285255938125-0.3134388054070.6163664851920.210645021733-0.01791515727681.322641444990.2319313428-0.3533111122010.6668168891920.0367987894420.71378471334731.399563852-29.4716139379.1784971339
21.08620471340.330340833958-0.1883566383991.02440113531-0.2386330112981.129377675810.216839412502-0.615743644885-0.04517464659150.460135863189-0.0980470717055-0.4622159878330.537617792910.416494198768-0.1683709928420.6668936840220.123476125803-0.3034692369480.762021472896-0.2800398991980.40631393579734.2029142492-7.1000383039882.7818198629
30.823103134185-0.00568046587377-0.2536883950630.7031424306490.4299362713330.8534846027180.0125502689584-0.1565139625560.1576466645140.05981753556010.04527108040590.0114897398478-0.07936785076710.09650986922360.162927256220.5113996249070.0123148078073-0.001918578811020.404425514689-0.3634411968830.41268862904427.349840278610.57827641272.0979418398
40.2557421485630.7111960507850.4287074428972.773562457990.5223094920381.292986517190.146948322599-0.197789587620.488534970159-0.1034048798720.05214100942810.17547065176-0.184096693364-0.006445131895260.04836736025750.3514448182420.0178785069695-0.02119861073770.346531573853-0.3264034401560.4830060238223.172585780212.673908074264.451234799
50.962517776767-0.0368948112577-0.23129446640.8695750624040.4388098942161.505984035550.0410128550556-0.0181562844660.480311169232-0.0802354801258-0.0205369024487-0.0730094673372-0.309872525263-0.1694423606720.009883073301550.158980996028-0.01817580286350.01095709539150.168197533239-0.01263744648430.28284771240324.74456206061.6608271406341.7575006187
60.9763962869660.2226299493810.5135743804122.30110712094-0.06124930996861.525757761670.1573960679350.19012409949-0.0325414654733-0.266483913683-0.085784530437-0.08322976888130.0607294410140.0606390365557-0.03760650666990.0835877758593-0.005174767090080.04738335662020.118095389948-0.004091798583430.13023260175831.6440387184-22.08615290529.0267103273
71.460582960780.761311888816-0.3191214117961.73539558783-0.1196146296441.19736996184-0.0929231314608-0.150998957722-0.5947617173620.03900739042260.17136373033-0.07806040975820.3143348601350.0577648313967-0.007437305835570.1931643486110.002417511936960.02478358863590.1653828613990.08954324520560.30013795254436.0894254942-42.113199180337.9913212003
87.21457402332-5.705046819434.569685374434.71310400406-3.512746271122.94490976807-0.0665841874123-0.1661878134280.08051777009140.3716297216910.1970574746180.05273453578640.0876463669047-0.153415617882-0.06843371359510.555028945407-0.162251849230.1928146729460.807992905483-0.1495033859380.45720785233-6.38172903131-15.978201090271.1581846648
92.14650856027-0.5001503704231.7661185290.716951862507-0.3322385752571.580797175210.2050799406140.0716866625369-0.210339259956-0.00770606212934-0.1282913927210.02481407361480.694452808314-0.0180637478736-0.05148156599620.817059000974-0.0632782736316-0.105412407480.5321135060610.02517450314810.1931721291554.48870231632-22.980015224871.2416466649
101.81033707374-2.37035861027-0.3596413968295.67495401377-0.8414468372254.33831886174-0.152620117428-0.5432717537810.2930464199280.3100646457060.1126433225410.141508727255-0.233798075396-0.716700356060.04746105022070.310907251959-0.05142597560150.05267695971470.5668078432-0.05737630827240.292931106412-4.1837412307-9.1972165251666.8389013887
116.60112979618-3.651865803620.8592621305712.65627302793-0.4757940659320.116480902367-0.143936359434-0.438396857270.1135449671290.5468842445570.2207252788490.106867593406-0.0715614306267-0.285631804538-0.08395315507150.3754396900110.04528446597130.0204144798230.410298089787-0.1186755708470.2448747768914.60936926838-7.8784943503970.4276428607
123.599959978991.607073253912.318099902391.246731233671.406466831041.822303918310.133201812186-0.142428572055-0.0693464222080.1771983689580.00354791452343-0.01222426283780.3157935963840.0448915946091-0.0483964533540.6331714896620.000975616923662-0.1266217513840.264486884881-0.07533441768390.17831701441413.9648489732-17.98008930963.5130230156
134.49212962664.122795929192.285362168993.783509501862.09706171321.162214677070.1691727626-0.295893913882-0.1792021487380.102673953069-0.203819462083-0.05318905883340.328186372881-0.2377564304240.005397890560960.481703321726-0.0427565800177-0.07413250348160.3004749420970.007870180211390.1791768731365.07928222786-22.346840525254.2046944061
143.29583766731-1.196930884150.004334599776063.405246503892.082844544753.904840897520.1850551107590.05075588481450.109542351114-0.1998564684520.219414089558-0.203990237882-0.1087062448730.095056604929-0.198661904980.478245458850.107552517919-0.1205616264850.357706955806-0.1572627914040.35564530520418.8683926135-5.770530328861.0689859959
153.31371983496-0.03289276271381.988328200271.164389475180.09027029386532.151273577750.0929144390149-0.289911316795-0.07317040356690.4551828148290.0162301016371-0.06213335038650.466655050601-0.0803106739043-0.1151408553360.4074031521290.00757569860013-0.01231453272920.235199922702-0.03948804333530.1474635378227.94008398902-13.40154478764.5134303298
160.296432720917-0.1672704356990.3837141972422.54074448033-0.3571479592222.952844473270.105650317061-0.480087682104-0.3251039146220.4946208640520.1563820228690.04818413962050.320123497597-0.169813199859-0.2355843166370.528947553315-0.0383526028038-0.01733231224980.298480653760.01191512894210.1597026570182.62310052879-20.79386260965.565469616
173.545370019521.07223634059-2.270986080351.81798398825-1.160583354842.22896946537-0.02175558470720.502188339171-0.536242035568-0.372585147626-0.1850333855940.146914358440.653432044027-0.165935732610.1461177232691.25553258014-0.0908178335888-0.2809379168520.520200841048-0.0009699035278230.580946611181-3.84585296194-20.0384502693-13.0970912858
180.947969580692-0.0266278420756-0.05873769118881.457831287390.342565360011.709167060460.1074311900030.3145698796370.15305679403-0.455195947225-0.04470957750590.5220803103610.0502341855247-0.438769740104-0.0892605201570.60668393106-0.0522174641354-0.2234990306230.4549674646080.2329117968190.472357054273-8.272960634965.21687459496-8.06016801047
191.76703759481-1.093344433410.02212836364363.3560690164-0.2121783202771.584017192770.1165380185980.08463318610280.657048215440.1367910315530.0779825661621-0.0149212319433-0.562923437165-0.0842445249667-0.1716724807250.5998640739550.0175883941874-0.04133808581120.2619536793420.1510468776450.506302683484-0.3835861665417.915220578412.1786322303
201.302642315440.0772388451721-0.2649731288691.3317559186-0.5499703620881.904327612120.0249544030005-0.06517202577330.3363589928620.117206926386-0.1261809133990.10538397859-0.386325231180.04766484948310.07094412115570.1694909238340.02021821707730.00470471941640.186056122411-0.01054037341060.24789350617-0.2861708666331.4105393310531.3074819889
210.1425193773630.2278178296680.309542679271.94092837667-0.08968591883761.274377048640.07196730761080.00383916398694-0.05563296767190.0601241103907-0.05071146549270.01998744372450.157796103150.0142075879571-0.03051135923560.06915155075450.01019697058340.01699329608220.159182131851-0.007161709020770.192593591462-3.63562022647-25.555172929937.2838440456
220.763704279189-0.640447821783-0.5782154887351.69972679380.1860450727750.947682988285-0.02185234210.315201849582-0.303185554915-0.2252177968040.0736772500698-0.1111636788470.4166435308510.0416549173444-0.04707247653670.3213492032740.0150713243877-0.008077729108060.258353797219-0.1391175785030.295094834385-5.47263750744-43.115085468923.023649558
231.738841359751.902298628792.262216602892.878949924413.051301256653.3591398099-0.04572153616180.223771732119-0.0286991058116-0.300522297724-0.143948716993-0.0803202475425-0.145854414032-0.1659853111980.07216777654030.544475665252-0.0372854209650.2321637285190.8666065078020.1073672181710.39691605979232.3628125696-3.90442435953-1.1808449753
241.623774983750.146194455941.466171078540.5741928220680.2795185344321.672650809830.3013749798020.0955562002992-0.19663094269-0.0926592856727-0.283216089651-0.09335085238310.671524451590.0784254396357-0.02575619537390.7400803416770.02803088395480.02058745701170.4548363628720.09944588210420.17083246312922.504719766-11.9650815111-3.18689376082
252.19275041831-0.4685641963761.857181284173.66329505554-0.7421725129386.3380532265-0.04704841441450.404006567330.415537973455-0.06174400271690.0278981571085-0.0784650080678-0.4070517184610.4071656261170.1424713775670.444049928401-0.0531776957293-0.001692355604450.4432871455010.1661492810420.39291486645229.43925759931.201387359864.78410973364
265.062353377692.828890659363.001702334022.132046171691.79961167181.83272166754-0.1253371069610.4419764961610.406453811375-0.4028380657590.10937747635-0.0153798571801-0.2418140541120.135705859650.01383566944330.477580515079-0.03344081721520.03292695323530.3250212505890.1619655818030.34139952166420.43723985392.273622017631.42131465621
271.86125102247-1.131606226761.190101863721.08303922547-0.7281333112820.8690678616770.03677127746730.09987143683330.0591376637768-0.1082581949150.005535401437830.03729451598850.225717254970.09302211906920.08884965675210.5770378468670.0130857458695-0.09356025920430.2165568063720.1185920491030.24329196262512.5715893063-10.46571097355.41342223231
283.08434493251-1.731496757961.447799429132.20362521183-1.002797888370.7429178346620.05630114425650.07201978799350.0973774310331-0.3584623395190.08038484729160.0613772151150.03656817285670.0910926218286-0.07752704382610.4573983259130.0218703164959-0.0355604140810.2951908665680.08872914289840.15526462092115.1121801257-8.7293522778312.3761790861
292.78461076875-0.3723887525831.775029550460.162401995396-0.248591496042.08880800279-0.1154447178560.1515292421690.181246627975-0.3008815746270.1030054858030.109301320955-0.1479587914940.09057945465190.09940680280780.5205907142380.015757439168-0.008032476932180.250177469920.1280818787120.27994638747417.8426942517-0.1615993506945.84084093738
305.642044040191.415960028271.036056658891.388276542380.3139109046150.193415859124-0.0019317873456-0.0352710079268-0.530686367559-0.3408252645090.007369649186090.1002209661640.3936983126380.216702077519-0.04247170085210.4808257763480.02291608926340.02476764488440.2928805479950.04037516174290.22805782757921.1034837393-12.32565807354.14916810399
311.323941874020.277214894528-0.9439022183410.1276192685-0.2443139524450.72835717379-0.282681803511-0.0983401309390.0955409446397-0.182308393777-0.0404695669031-0.02445269776910.3975869195230.0966140377090.3722098186770.325415588443-0.00817457003710.04734911221660.3665754632480.01558469519350.33557829903913.0639692901-10.374773930734.9879478284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 289 )
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 515 )
7X-RAY DIFFRACTION7chain 'A' and (resid 516 through 618 )
8X-RAY DIFFRACTION8chain 'C' and (resid 21 through 29 )
9X-RAY DIFFRACTION9chain 'C' and (resid 30 through 44 )
10X-RAY DIFFRACTION10chain 'C' and (resid 45 through 55 )
11X-RAY DIFFRACTION11chain 'C' and (resid 56 through 66 )
12X-RAY DIFFRACTION12chain 'C' and (resid 67 through 82 )
13X-RAY DIFFRACTION13chain 'C' and (resid 83 through 93 )
14X-RAY DIFFRACTION14chain 'C' and (resid 94 through 102 )
15X-RAY DIFFRACTION15chain 'C' and (resid 103 through 143 )
16X-RAY DIFFRACTION16chain 'C' and (resid 144 through 156 )
17X-RAY DIFFRACTION17chain 'B' and (resid 27 through 59 )
18X-RAY DIFFRACTION18chain 'B' and (resid 60 through 238 )
19X-RAY DIFFRACTION19chain 'B' and (resid 239 through 289 )
20X-RAY DIFFRACTION20chain 'B' and (resid 290 through 437 )
21X-RAY DIFFRACTION21chain 'B' and (resid 438 through 515 )
22X-RAY DIFFRACTION22chain 'B' and (resid 516 through 619 )
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 29 )
24X-RAY DIFFRACTION24chain 'D' and (resid 30 through 44 )
25X-RAY DIFFRACTION25chain 'D' and (resid 45 through 55 )
26X-RAY DIFFRACTION26chain 'D' and (resid 56 through 66 )
27X-RAY DIFFRACTION27chain 'D' and (resid 67 through 82 )
28X-RAY DIFFRACTION28chain 'D' and (resid 83 through 102 )
29X-RAY DIFFRACTION29chain 'D' and (resid 103 through 128 )
30X-RAY DIFFRACTION30chain 'D' and (resid 129 through 156 )
31X-RAY DIFFRACTION31chain 'A' and resid 709 or chain 'B' and (resid 701 through 702) or chain 'D' and resid 201

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