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- PDB-4y2d: Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex -

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Basic information

Entry
Database: PDB / ID: 4y2d
TitleCrystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex
Components
  • (Chimeric TCR ...) x 2
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of macrophage activation ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of macrophage activation / positive thymic T cell selection / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / lysosome / early endosome / learning or memory / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
: / : / MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / : / MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7DW / alpha-L-fucopyranose / T cell receptor alpha variable 11 / Beta-chain / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsZajonc, D.M. / Yu, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074952 United States
CitationJournal: To Be Published
Title: Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells
Authors: Birkholz, A. / Nemcovic, M. / Yu, E.D. / Girardi, E. / Wang, J. / Khurana, A. / Pauwels, N. / Franck, R.W. / Tsuji, M. / Howell, A. / Calenbergh, S. / Kronenberg, M. / Zajonc, D.M.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 29, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_atoms / 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_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_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.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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_alt_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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93017
Polymers188,7518
Non-polymers3,1799
Water00
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7818
Polymers94,3764
Non-polymers1,4064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1499
Polymers94,3764
Non-polymers1,7735
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.422, 150.264, 100.800
Angle α, β, γ (deg.)90.000, 96.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 280
2114E1 - 280
1124B1 - 100
2124F1 - 100
1134C1 - 210
2134G1 - 210
1144D1 - 250
2144H1 - 250

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.997578, -0.033907, 0.060737), (0.033131, -0.999357, -0.013742), (0.061164, -0.011697, 0.998059)24.86112, -37.81958, -0.19629
3given(1), (1), (1)
4given(-0.996659, -0.04813, 0.065985), (0.047908, -0.998839, -0.004938), (0.066146, -0.001761, 0.997808)24.14159, -38.582081, 0.00479
5given(1), (1), (1)
6given(-0.999713, -0.00016, 0.02395), (0.000169, -1, 0.000354), (0.02395, 0.000358, 0.999713)27.228661, -38.245419, 0.55387
7given(1), (1), (1)
8given(-0.999918, -0.001527, 0.012746), (0.001457, -0.999984, -0.005499), (0.012754, -0.00548, 0.999904)27.98807, -37.80426, 0.12503

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: Ectodomain, UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P11609
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01887

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Chimeric TCR ... , 2 types, 4 molecules CGDH

#3: Protein Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) / Protein Trav11d / Human nkt tcr beta chain


Mass: 23055.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: Trav11, Trav11d, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0A0B4J1J9*PLUS
#4: Protein Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain) / Beta-chain / T-cell receptor beta-2 chain C region


Mass: 27026.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: TRBC2, TCRBC2 / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A2NTY6*PLUS

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Sugars , 3 types, 7 molecules

#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.: 1 / Source method: obtained synthetically
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: 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.: 5 / Source method: obtained synthetically / 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
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-7DW / 11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide


Mass: 742.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H72FNO9

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Details

Sequence detailsChimeric TCR Valpha14Jalpha18 chain (chain C) is made of: Mouse variable domain ...Chimeric TCR Valpha14Jalpha18 chain (chain C) is made of: Mouse variable domain (MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVI) and Human constant domain (PDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS) Chimeric TCR Vbeta8.2 chain (chain D) is made of: Mouse variable domain (MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSK) and Human constant domain (AEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA)

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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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 4000, 8% tascimate pH 4.0 / PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 44418 / % possible obs: 99.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Χ2: 1.373 / Net I/av σ(I): 13.194 / Net I/σ(I): 7.9 / Num. measured all: 135018
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.1230.53629501.02999.8
3.12-3.230.43329751.04499.8
3.2-3.2930.3429331.11799.5
3.29-3.3830.2629641.18999.8
3.38-3.4930.20729651.23399.8
3.49-3.6230.17929931.25599.9
3.62-3.7630.14929711.36299.8
3.76-3.9330.12629441.47999.9
3.93-4.1430.10529721.62799.7
4.14-4.430.08629901.81699.7
4.4-4.743.10.07129501.82399.5
4.74-5.213.10.06529641.62299.2
5.21-5.9730.06729551.46398.9
5.97-7.513.10.05729661.37698.2
7.51-503.10.03129261.14396.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7Y and 3QUZ

2q7y

3quz


Resolution: 3.05→49.41 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 45.123 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1388 3.1 %RANDOM
Rwork0.2168 43007 --
obs0.2181 43007 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.39 Å2 / Biso mean: 70.5 Å2 / Biso min: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.19 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 3.05→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11627 0 316 0 11943
Biso mean--74.1 --
Num. residues----1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212272
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210655
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.9516783
X-RAY DIFFRACTIONr_angle_other_deg0.8033.01324344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59751541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4524.217517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.081151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3831550
X-RAY DIFFRACTIONr_chiral_restr0.0560.21890
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022890
X-RAY DIFFRACTIONr_mcbond_it0.4682.416218
X-RAY DIFFRACTIONr_mcbond_other0.4682.416217
X-RAY DIFFRACTIONr_mcangle_it0.8393.6157741
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3232MEDIUM POSITIONAL0.250.5
1A3232MEDIUM THERMAL1.942
2B1041MEDIUM POSITIONAL0.290.5
2B1041MEDIUM THERMAL2.582
3C2815MEDIUM POSITIONAL0.20.5
3C2815MEDIUM THERMAL1.212
4D3434MEDIUM POSITIONAL0.230.5
4D3434MEDIUM THERMAL1.132
LS refinement shellResolution: 3.051→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 104 -
Rwork0.315 3126 -
all-3230 -
obs--99.26 %
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)
13.81351.20980.90963.37620.28611.7833-0.05380.5185-0.4639-0.30350.0245-0.08090.1327-0.14940.02930.3370.0555-0.03220.4081-0.12220.379919.5720.47722.841
20.5868-0.5114-0.99465.7588-1.13422.61380.11870.77660.2315-1.06350.41640.0905-0.1393-1.427-0.53510.7864-0.0974-0.23232.3363-0.01210.3684-9.5061.9743.674
310.97992.7683-0.28552.3380.11882.2134-0.27360.7375-0.1499-0.00890.24130.31780.3126-0.6160.03240.40250.0149-0.10270.7924-0.16170.4239-8.857-1.24723.03
45.8103-1.91852.17572.3375-0.75181.9373-0.06360.17-0.12310.1522-0.0176-0.05340.0320.07360.08120.2432-0.006-0.0630.2332-0.06190.309747.721-7.8441.903
52.2673-0.95321.55833.4061-0.6817.107-0.1121-0.57140.20370.44780.11620.0141-0.4252-0.1172-0.00410.3669-0.0079-0.01490.3727-0.13070.342535.3116.37755.951
64.0748-0.152-1.88465.56081.95085.0133-0.0273-0.1803-0.37560.92130.0864-0.24321.11050.5142-0.05910.7270.0521-0.30690.4884-0.05860.685970.427-10.01769.569
76.617-0.5256-0.65823.50421.03263.98440.0364-0.3594-0.56510.5995-0.0893-0.01540.2946-0.06830.05280.5264-0.0488-0.16580.3228-0.03790.30160.5464.00472.257
82.7454-0.0542-1.54034.78280.38382.65060.13590.04710.0747-0.99960.1645-0.5595-0.30870.2784-0.30040.5119-0.03450.17830.3302-0.07350.3767.87-38.42922.034
95.25890.8166-2.04822.4682.5425.40220.27960.44080.2851-0.47780.3783-0.5669-0.19090.553-0.65791.0172-0.21440.76691.0546-0.22991.064834.294-37.9431.099
104.27590.44241.89060.25020.29992.77710.022-0.3874-0.1906-0.23490.1885-0.6195-0.37431.0247-0.21050.5939-0.23810.72910.9773-0.48641.796234.689-36.57120.958
115.4767-2.6059-2.8973.9171.26222.682-0.00740.1308-0.1083-0.0968-0.06070.388-0.0652-0.01680.06810.2061-0.0035-0.07470.20530.02470.2674-19.466-30.47741.967
121.695-0.4686-1.10162.45840.29087.0196-0.1788-0.401-0.23470.5845-0.0635-0.08730.58440.30970.24220.35370.0104-0.01470.3850.11030.3194-6.704-44.43255.591
134.9661-1.64821.04424.6381-2.46856.6938-0.0623-0.11750.71971.12470.16030.5085-1.4101-0.63-0.0980.76190.02870.34970.4135-0.00460.8282-41.59-28.39470.181
145.9750.1461.11773.9601-1.02713.96540.1542-0.32990.37170.6185-0.1880.1578-0.3469-0.0310.03380.4971-0.07230.12490.29950.02810.2212-31.969-42.36671.964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 185
2X-RAY DIFFRACTION1A302 - 303
3X-RAY DIFFRACTION1E505
4X-RAY DIFFRACTION1A304
5X-RAY DIFFRACTION2A186 - 275
6X-RAY DIFFRACTION3B1 - 97
7X-RAY DIFFRACTION4C2 - 114
8X-RAY DIFFRACTION5D2 - 112
9X-RAY DIFFRACTION6C115 - 204
10X-RAY DIFFRACTION7D113 - 240
11X-RAY DIFFRACTION8E6 - 185
12X-RAY DIFFRACTION8A301
13X-RAY DIFFRACTION8E501 - 504
14X-RAY DIFFRACTION8E506
15X-RAY DIFFRACTION9E186 - 275
16X-RAY DIFFRACTION10F2 - 97
17X-RAY DIFFRACTION11G2 - 114
18X-RAY DIFFRACTION12H2 - 112
19X-RAY DIFFRACTION13G115 - 204
20X-RAY DIFFRACTION14H113 - 240

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