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- PDB-6mjq: Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex -

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Basic information

Entry
Database: PDB / ID: 6mjq
TitleCrystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
  • T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein
Keywordsimmune system/inhibitor / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor / IMMUNE SYSTEM / immune system-inhibitor complex
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 / alpha-beta T cell receptor complex ...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 / alpha-beta T cell receptor complex / 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 / alpha-beta T cell activation / 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 / T cell receptor signaling pathway / 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 / cell surface receptor signaling pathway / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant 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 ...: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant 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-JUD / T cell receptor alpha variable 11 / CD1d1 antigen / T cell receptor beta constant 2 / Tcell receptor chain / Beta-chain / Human nkt tcr alpha 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 Å
AuthorsZajonc, D.M. / Bitra, A. / Janssens, J.
CitationJournal: ChemMedChem / Year: 2019
Title: 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Authors: Janssens, J. / Bitra, A. / Wang, J. / Decruy, T. / Venken, K. / van der Eycken, J. / Elewaut, D. / Zajonc, D.M. / van Calenbergh, S.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein
D: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
E: Antigen-presenting glycoprotein CD1d1
G: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein
H: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,25122
Polymers188,7518
Non-polymers5,50014
Water1,820101
1
C: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein
D: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,88510
Polymers94,3764
Non-polymers2,5106
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
G: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein
H: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,36612
Polymers94,3764
Non-polymers2,9908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.967, 191.858, 150.957
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21G
12D
22H
13A
23E
14B
24F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSERCA2 - 2043 - 205
21THRTHRSERSERGF2 - 2043 - 205
12ALAALAARGARGDB2 - 2393 - 240
22ALAALAARGARGHG2 - 2393 - 240
13LYSLYSTRPTRPAC6 - 2796 - 279
23LYSLYSTRPTRPEE6 - 2796 - 279
14LYSLYSMETMETBD3 - 993 - 99
24LYSLYSMETMETFH3 - 993 - 99

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules CGDHAEBF

#1: Protein T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, chimeric protein / T cell receptor alpha variable 11D / 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 (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav11, Trav11d, Traj18, B2M, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J1J9, UniProt: K7N5M3
#2: Protein Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN


Mass: 27026.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Plasmid: pET22b+ / Gene: TRBC2, TCRBC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A2NTY6, UniProt: A0N8J3, UniProt: A0A5B9
#3: Protein Antigen-presenting glycoprotein CD1d1 / MCG3074 / isoform CRA_a


Mass: 32632.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, mCG_3074 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0R4J090, UniProt: P11609*PLUS
#4: Protein Beta-2-microglobulin


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

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Sugars , 4 types, 6 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[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
#7: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_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]{}}}[(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.: 1
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 , 4 types, 109 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-JUD / N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide


Mass: 1016.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C58H104F3NO9
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 m sodium malonate pH 4.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 42754 / % possible obs: 96.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.072 / Rrim(I) all: 0.147 / Χ2: 1.46 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.30.33540150.8660.2030.3940.56590.9
3.11-3.233.40.27841370.9110.1680.3280.61493.6
3.23-3.383.40.22741810.9270.140.2690.69194.7
3.38-3.563.80.19643420.9530.1130.2280.8697.9
3.56-3.783.90.16743070.9580.0960.1941.02597.6
3.78-4.073.70.13343100.9780.0770.1541.13897
4.07-4.483.90.10643440.9840.0590.1221.40298
4.48-5.1340.09143480.990.050.1041.45698.2
5.13-6.4640.09943740.9840.0550.1141.33398
6.46-5040.10243960.9360.0570.1174.75797.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRS

4irs


Resolution: 3→49.75 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.579 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 2142 5 %RANDOM
Rwork0.2154 ---
obs0.2175 40603 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.6 Å2 / Biso mean: 52.394 Å2 / Biso min: 18.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.73 Å2
2--3.38 Å20 Å2
3----3.9 Å2
Refinement stepCycle: final / Resolution: 3→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12766 0 370 101 13237
Biso mean--66.14 38.28 -
Num. residues----1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01413528
X-RAY DIFFRACTIONr_bond_other_d0.0010.01811567
X-RAY DIFFRACTIONr_angle_refined_deg0.7111.6918420
X-RAY DIFFRACTIONr_angle_other_deg0.6351.69127215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84451619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92322.787689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.002152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0441570
X-RAY DIFFRACTIONr_chiral_restr0.0290.21788
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022559
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C56870.03
12G56870.03
21D73550.04
22H73550.04
31A85000.05
32E85000.05
41B28570.04
42F28570.04
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 126 -
Rwork0.318 2348 -
all-2474 -
obs--75.73 %

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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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