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- PDB-2po6: Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Mic... -

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Basic information

Entry
Database: PDB / ID: 2po6
TitleCrystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain
Components
  • Beta-2-microglobulin
  • NKT15 alpha-chain
  • NKT15 beta-chain
  • T-cell surface glycoprotein CD1d
KeywordsLIPID BINDING PROTEIN/IMMUNE SYSTEM / CD1d-lipid antigen NKT15 complex / LIPID BINDING PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / beta-2-microglobulin binding / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
T-cell receptor alpha chain, constant domain / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...T-cell receptor alpha chain, constant domain / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AGH / T cell receptor alpha chain constant / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin / : / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBorg, N.A.
CitationJournal: Nature / Year: 2007
Title: CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor.
Authors: Borg, N.A. / Wun, K.S. / Kjer-Nielsen, L. / Wilce, M.C. / Pellicci, D.G. / Koh, R. / Besra, G.S. / Bharadwaj, M. / Godfrey, D.I. / McCluskey, J. / Rossjohn, J.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 29, 2014Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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 / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_chiral.auth_seq_id
Remark 999Sequence No suitable database references were found for chains C,G,D and H at time of processing. ...Sequence No suitable database references were found for chains C,G,D and H at time of processing.(Kjer-Nielsen, L., Borg, N.A., et al., J. exp med. 203 (3) 661-673), 2006

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
C: NKT15 alpha-chain
D: NKT15 beta-chain
E: T-cell surface glycoprotein CD1d
F: Beta-2-microglobulin
G: NKT15 alpha-chain
H: NKT15 beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,07615
Polymers187,8888
Non-polymers3,1887
Water00
1
A: T-cell surface glycoprotein CD1d
B: Beta-2-microglobulin
C: NKT15 alpha-chain
D: NKT15 beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6288
Polymers93,9444
Non-polymers1,6844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-55 kcal/mol
Surface area39370 Å2
MethodPISA
2
E: T-cell surface glycoprotein CD1d
F: Beta-2-microglobulin
G: NKT15 alpha-chain
H: NKT15 beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4487
Polymers93,9444
Non-polymers1,5043
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-52 kcal/mol
Surface area38860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.012, 155.636, 85.981
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
12B
22B
13C
23C
14D
24D
15D
25D
16E
26E
17F
27F
18G
28G
19G
29G
110C
210C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHISHISAA6 - 2801 - 275
21ARGARGHISHISAA6 - 2801 - 275
12ILEILEMETMETBB1 - 991 - 99
22ILEILEMETMETBB1 - 991 - 99
13ASNASNASPASPCC1 - 1171 - 114
23ASNASNASPASPCC1 - 1171 - 114
14ALAALATHRTHRDD2 - 1171 - 114
24ALAALATHRTHRDD2 - 1171 - 114
15GLUGLUASPASPDD118 - 247115 - 244
25GLUGLUASPASPDD118 - 247115 - 244
16ARGARGTRPTRPEE6 - 2771 - 272
26ARGARGTRPTRPEE6 - 2771 - 272
17GLNGLNMETMETFF2 - 992 - 99
27GLNGLNMETMETFF2 - 992 - 99
18ASNASNASPASPGG1 - 1171 - 114
28ASNASNASPASPGG1 - 1171 - 114
19ILEILEPROPROGG118 - 207115 - 204
29ILEILEPROPROGG118 - 207115 - 204
110ILEILESERSERCC118 - 206115 - 203
210ILEILESERSERCC118 - 206115 - 203

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 3 types, 6 molecules AEBFDH

#1: Protein T-cell surface glycoprotein CD1d / CD1d antigen / R3G1


Mass: 31758.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastbac dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2 / Fragment: beta-2-microglobulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pFastbac dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769
#4: Protein NKT15 beta-chain


Mass: 27772.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GMR4

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Antibody , 1 types, 2 molecules CG

#3: Antibody NKT15 alpha-chain


Mass: 22664.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIZ8, UniProt: P01848*PLUS

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Sugars , 4 types, 7 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#6: 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 / Details: chemical entity
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Details: chemical entity
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-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9

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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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 42581 / % possible obs: 95.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.138 / Χ2: 1.434 / Net I/σ(I): 6.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.486 / Num. unique all: 3310 / Χ2: 0.934 / % possible all: 74.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)

2eys

1zt4


Resolution: 3.2→29.18 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.833 / SU B: 58.18 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2135 5.1 %RANDOM
Rwork0.226 ---
obs0.229 42133 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.14 Å2
2---0.01 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13083 0 215 0 13298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02113667
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9518583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98451631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06924.15653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.437152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6051581
X-RAY DIFFRACTIONr_chiral_restr0.0850.22010
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210429
X-RAY DIFFRACTIONr_nbd_refined0.1980.25412
X-RAY DIFFRACTIONr_nbtor_refined0.3030.28965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.23
X-RAY DIFFRACTIONr_mcbond_it0.2161.58372
X-RAY DIFFRACTIONr_mcangle_it0.396213253
X-RAY DIFFRACTIONr_scbond_it0.47636091
X-RAY DIFFRACTIONr_scangle_it0.8334.55330
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeWeight position
11A2192X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
11A2192X-RAY DIFFRACTIONMEDIUM THERMAL2
21B824X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
21B824X-RAY DIFFRACTIONMEDIUM THERMAL2
31C885X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
31C885X-RAY DIFFRACTIONMEDIUM THERMAL2
41D910X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
41D910X-RAY DIFFRACTIONMEDIUM THERMAL2
51D1047X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
51D1047X-RAY DIFFRACTIONMEDIUM THERMAL2
61E2171X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
61E2171X-RAY DIFFRACTIONMEDIUM THERMAL2
71F813X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
71F813X-RAY DIFFRACTIONMEDIUM THERMAL2
81G885X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
81G885X-RAY DIFFRACTIONMEDIUM THERMAL2
91G703X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
91G703X-RAY DIFFRACTIONMEDIUM THERMAL2
101C696X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
101C696X-RAY DIFFRACTIONMEDIUM THERMAL2
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 115 -
Rwork0.318 2278 -
obs-2393 74.71 %
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)
14.45180.5319-4.58373.6746-3.04168.3658-0.0009-0.2881-0.0648-0.0715-0.0662-0.23740.20910.58940.0672-0.3949-0.0744-0.0877-0.3624-0.0177-0.240943.398-6.64735.377
212.89592.19724.846610.41-0.65158.3956-0.3517-0.5801-0.36940.032-0.00330.37450.1739-0.69750.355-0.2646-0.05250.2099-0.1978-0.0183-0.270213.293-9.68953.683
317.33841.8908-4.36053.934-0.39895.44780.05480.67050.14570.0372-0.13690.12830.2033-0.50990.0821-0.2781-0.03590.057-0.30880.0822-0.309531.9088.19923.016
44.3057-0.47892.07263.3919-0.021612.1299-0.318-0.03980.43950.0671-0.16140.15810.0212-0.71340.4794-0.45870.00160.0518-0.2692-0.0818-0.079411.6335.44445.489
52.12870.1825-2.38211.1482-1.37264.5594-0.4132-0.2964-0.2734-0.3456-0.1668-0.53620.61520.71230.58-0.06820.08760.1634-0.28470.06970.034775.1274.427-0.343
63.7652-1.6095-2.0822.5022.57439.3654-0.2470.9933-0.3817-0.9126-0.26810.04220.7151-0.78690.51510.4183-0.09310.2606-0.016-0.0012-0.032569.6491.9-18.981
73.6942-0.4542.79922.97312.3339.5351-0.1115-0.04020.11290.05940.00910.375-0.4416-0.51730.1024-0.4102-0.01440.0947-0.4175-0.0021-0.238552.66249.38536.353
813.43892.5525-2.863210.2852.13147.4187-0.1955-0.68490.3430.37780.2821-0.5473-0.08860.7669-0.0866-0.09090.0818-0.1027-0.19240.0195-0.394279.14752.47659.695
912.64132.46384.38855.22831.41117.3032-0.11780.44010.0541-0.0432-0.07230.0401-0.05430.63230.1901-0.3925-0.00160.0085-0.3703-0.0061-0.298166.10734.65425.964
105.8962-1.0913-3.00183.95071.145410.8923-0.0914-0.0469-0.4070.4906-0.0347-0.1229-0.16670.27290.1261-0.4516-0.0017-0.0581-0.35410.0677-0.263782.33537.55551.696
111.9926-0.17322.15870.98171.2195.5572-0.1372-0.18450.1161-0.3775-0.26440.4148-0.617-0.8040.4015-0.15990.0644-0.1093-0.2886-0.0397-0.024927.50738.383-4.342
123.9038-1.04241.32823.7428-3.041411.248-0.01381.04710.5098-0.9091-0.4715-0.2606-0.62010.93380.48530.1704-0.0113-0.1532-0.05740.0331-0.102635.94241.041-21.734
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CC1 - 1171 - 114
22CC118 - 205115 - 202
33DD3 - 1172 - 114
44DD118 - 247115 - 244
55AA6 - 2801 - 275
66BB1 - 991 - 99
77GG1 - 1171 - 114
88GG118 - 205115 - 202
99HH3 - 1172 - 114
1010HH118 - 247115 - 244
1111EE6 - 2771 - 272
1212FF2 - 992 - 99

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