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- PDB-6rpb: Crystal structure of the T-cell receptor NYE_S1 bound to HLA A2*0... -

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Basic information

Entry
Database: PDB / ID: 6rpb
TitleCrystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Heteroclitic NY-ESO-1 157-165 peptide
KeywordsIMMUNE SYSTEM / T-cell receptor / peptide-Human leukocyte antigen complex / NY-ESO-1 / cancer testis antigen
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / 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 / RNA binding
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...CTAG/Pcc1 family / Transcription factor Pcc1 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsColes, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. ...Coles, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Vuidepot, A. / Jakobsen, B.K. / Harper, S.
CitationJournal: J Immunol. / Year: 2020
Title: TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex.
Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / ...Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / Chester, F. / Wiederhold, K. / Robinson, R.A. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Jakobsen, B.K. / Vuidepot, A. / Harper, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Heteroclitic NY-ESO-1 157-165 peptide
D: T-cell receptor alpha chain
E: T-cell receptor beta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Heteroclitic NY-ESO-1 157-165 peptide
I: T-cell receptor alpha chain
J: T-cell receptor beta chain
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
M: Heteroclitic NY-ESO-1 157-165 peptide
N: T-cell receptor alpha chain
O: T-cell receptor beta chain
P: HLA class I histocompatibility antigen, A-2 alpha chain
Q: Beta-2-microglobulin
R: Heteroclitic NY-ESO-1 157-165 peptide
S: T-cell receptor alpha chain
T: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)381,18720
Polymers381,18720
Non-polymers00
Water4,125229
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Heteroclitic NY-ESO-1 157-165 peptide
D: T-cell receptor alpha chain
E: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,2975
Polymers95,2975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Heteroclitic NY-ESO-1 157-165 peptide
I: T-cell receptor alpha chain
J: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,2975
Polymers95,2975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
M: Heteroclitic NY-ESO-1 157-165 peptide
N: T-cell receptor alpha chain
O: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,2975
Polymers95,2975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: HLA class I histocompatibility antigen, A-2 alpha chain
Q: Beta-2-microglobulin
R: Heteroclitic NY-ESO-1 157-165 peptide
S: T-cell receptor alpha chain
T: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,2975
Polymers95,2975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.342, 77.134, 184.632
Angle α, β, γ (deg.)93.02, 93.45, 108.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12A
22K
13A
23P
14B
24G
15B
25L
16B
26Q
17D
27I
18D
28N
19D
29S
110E
210J
111E
211O
112E
212T
113F
213K
114F
214P
115G
215L
116G
216Q
117I
217N
118I
218S
119J
219O
120J
220T
121K
221P
122L
222Q
123N
223S
124O
224T

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
11GLYGLYPROPROAA1 - 2762 - 277
21GLYGLYPROPROFF1 - 2762 - 277
12GLYGLYTRPTRPAA1 - 2742 - 275
22GLYGLYTRPTRPKK1 - 2742 - 275
13GLYGLYGLUGLUAA1 - 2752 - 276
23GLYGLYGLUGLUPP1 - 2752 - 276
14METMETMETMETBB0 - 991 - 100
24METMETMETMETGG0 - 991 - 100
15METMETMETMETBB0 - 991 - 100
25METMETMETMETLL0 - 991 - 100
16METMETMETMETBB0 - 991 - 100
26METMETMETMETQQ0 - 991 - 100
17GLUGLUPROPRODD3 - 2194 - 203
27GLUGLUPROPROII3 - 2194 - 203
18GLUGLUPROPRODD3 - 2174 - 201
28GLUGLUPROPRONN3 - 2174 - 201
19GLUGLUPROPRODD3 - 2174 - 201
29GLUGLUPROPROSS3 - 2174 - 201
110GLYGLYARGARGEE3 - 2564 - 242
210GLYGLYARGARGJJ3 - 2564 - 242
111GLYGLYALAALAEE3 - 2534 - 239
211GLYGLYALAALAOO3 - 2534 - 239
112GLYGLYGLYGLYEE3 - 2554 - 241
212GLYGLYGLYGLYTT3 - 2554 - 241
113GLYGLYARGARGFF1 - 2732 - 274
213GLYGLYARGARGKK1 - 2732 - 274
114GLYGLYGLUGLUFF1 - 2752 - 276
214GLYGLYGLUGLUPP1 - 2752 - 276
115METMETMETMETGG0 - 991 - 100
215METMETMETMETLL0 - 991 - 100
116METMETMETMETGG0 - 991 - 100
216METMETMETMETQQ0 - 991 - 100
117GLUGLUPROPROII3 - 2174 - 201
217GLUGLUPROPRONN3 - 2174 - 201
118GLUGLUPROPROII3 - 2174 - 201
218GLUGLUPROPROSS3 - 2174 - 201
119GLYGLYALAALAJJ3 - 2534 - 239
219GLYGLYALAALAOO3 - 2534 - 239
120GLYGLYGLYGLYJJ3 - 2554 - 241
220GLYGLYGLYGLYTT3 - 2554 - 241
121GLYGLYTRPTRPKK1 - 2742 - 275
221GLYGLYTRPTRPPP1 - 2742 - 275
122METMETMETMETLL0 - 991 - 100
222METMETMETMETQQ0 - 991 - 100
123GLUGLUPROPRONN3 - 2174 - 201
223GLUGLUPROPROSS3 - 2174 - 201
124GLYGLYALAALAOO3 - 2534 - 239
224GLYGLYALAALATT3 - 2534 - 239

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

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Components

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Protein , 2 types, 8 molecules AFKPBGLQ

#1: Protein
HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 32082.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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T-cell receptor ... , 2 types, 8 molecules DINSEJOT

#4: Protein
T-cell receptor alpha chain


Mass: 22871.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein
T-cell receptor beta chain


Mass: 27373.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 233 molecules CHMR

#3: Protein/peptide
Heteroclitic NY-ESO-1 157-165 peptide


Mass: 1090.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.5→73.11 Å / Num. obs: 125234 / % possible obs: 96.9 % / Redundancy: 1.7 % / CC1/2: 0.971 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.094 / Net I/σ(I): 2.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9382 / CC1/2: 0.767 / Rpim(I) all: 0.41 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia20.5.474-gb1e580cd-dials-1.8data reduction
xia20.5.474-gb1e580cd-dials-1.8data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e00 and 4FTV

5e00

4ftv


Resolution: 2.5→73.09 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.88 / SU B: 42.848 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R: 0.724 / ESU R Free: 0.321 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27271 6543 5 %RANDOM
Rwork0.24911 ---
obs0.25028 125234 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20.95 Å2-0.6 Å2
2--1.44 Å20.69 Å2
3----2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.5→73.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25965 0 0 229 26194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01926691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0223259
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.92936251
X-RAY DIFFRACTIONr_angle_other_deg0.842354058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94453199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12223.691355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.466154260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.48915190
X-RAY DIFFRACTIONr_chiral_restr0.070.23801
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02129860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025810
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3461.92412892
X-RAY DIFFRACTIONr_mcbond_other0.3461.92412891
X-RAY DIFFRACTIONr_mcangle_it0.652.88316059
X-RAY DIFFRACTIONr_mcangle_other0.652.88316060
X-RAY DIFFRACTIONr_scbond_it0.1911.93213799
X-RAY DIFFRACTIONr_scbond_other0.1911.93213800
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3752.88920193
X-RAY DIFFRACTIONr_long_range_B_refined1.76620.99927464
X-RAY DIFFRACTIONr_long_range_B_other1.75420.98627452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A171480.04
12F171480.04
21A166020.03
22K166020.03
31A172420.04
32P172420.04
41B62020.03
42G62020.03
51B62040.01
52L62040.01
61B61800.03
62Q61800.03
71D111180.04
72I111180.04
81D108900.04
82N108900.04
91D109080.04
92S109080.04
101E149460.04
102J149460.04
111E146420.04
112O146420.04
121E148220.04
122T148220.04
131F163160.03
132K163160.03
141F171840.03
142P171840.03
151G61960.03
152L61960.03
161G61680.04
162Q61680.04
171I108860.04
172N108860.04
181I109240.03
182S109240.03
191J146860.04
192O146860.04
201J148860.03
202T148860.03
211K166660.02
212P166660.02
221L61940.03
222Q61940.03
231N109520.02
232S109520.02
241O147280.03
242T147280.03
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 412 -
Rwork0.349 8970 -
obs--92.63 %
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)
10.7833-0.27630.6162.1179-1.97522.5128-0.0381-0.0639-0.1816-0.06370.0441-0.11510.12330.0572-0.00590.4125-0.15460.12780.2295-0.03570.09335.06640.681799.1617
23.6983-0.37242.5151.7756-0.75297.6488-0.0766-0.43860.08350.24860.0536-0.0638-0.1046-0.21040.0230.3426-0.0360.12490.1602-0.00420.07540.74916.8005116.9779
30.6516-1.63950.65274.1721-1.9152.36340.07040.10060.0424-0.1722-0.2493-0.1461-0.02840.18830.17890.2664-0.04750.0530.2423-0.00770.16325.71212.819583.3429
41.0244-1.00850.34244.2081-1.88413.06710.03120.19470.1165-0.3785-0.1734-0.174-0.08130.05560.14220.3424-0.12150.11760.29080.00090.07188.767133.54950.319
50.5624-0.73390.37312.5725-1.44721.45760.06620.07240.24910.0494-0.2378-0.0415-0.1081-0.04950.17160.3198-0.17090.10210.2608-0.06860.2293.674745.782265.3403
63.17790.2063-2.38890.90310.0652.77740.0302-0.1078-0.05710.02520.0044-0.26440.01260.1756-0.03460.2933-0.13110.00790.19420.02390.087944.596456.420583.9178
72.6919-0.7554-1.80453.45831.85537.63690.09080.3888-0.0583-0.3163-0.0992-0.0272-0.1476-0.20970.00840.2256-0.05640.03410.26340.05460.037637.503458.585965.9828
86.4557-1.52480.03530.524-0.89194.7856-0.2979-0.0899-0.16030.0544-0.0062-0.02590.12640.10030.30410.2592-0.0533-0.01840.20240.04720.183232.073352.317499.5902
93.93960.25-1.77530.9615-0.48863.1153-0.1036-0.4276-0.2540.16890.00390.1650.0577-0.07710.09970.4246-0.0850.03550.29280.08960.072213.796943.263132.8346
102.5952-0.1637-1.38390.4456-0.14341.6898-0.2392-0.159-0.26460.0330.04760.1990.0418-0.17860.19160.4068-0.14010.04160.24780.00960.14370.284644.4906118.1741
111.25450.01831.48941.2806-0.49343.785-0.0202-0.04790.1987-0.09080.05610.2835-0.0079-0.4916-0.03590.3633-0.13810.08930.35020.01180.1425.442214.1174-5.1174
122.9311-0.5959-0.13634.923-2.46056.46060.00770.30470.3453-0.327-0.1083-0.13560.09880.00550.10060.2957-0.13740.07960.3548-0.02480.065713.818513.8912-23.2431
135.27950.67572.6560.3504-0.63544.9425-0.2559-0.09820.33540.066-0.00420.0203-0.4723-0.0940.26010.3099-0.02540.01470.2257-0.02570.13914.525615.68811.1038
143.67420.31251.9560.46960.17634.1343-0.0949-0.3804-0.03380.1967-0.0671-0.02620.10050.07950.1620.4637-0.05950.13370.2180.00720.063627.334221.099146.7147
153.13540.19561.69950.09580.49392.795-0.19-0.2026-0.07960.04050.10560.02060.24020.33590.08430.5059-0.05260.12450.29560.02950.03843.361523.10533.9765
161.0322-0.0293-0.79781.56181.56063.54620.0367-0.02470.2504-0.0125-0.02220.2061-0.4053-0.1508-0.01460.4541-0.06920.02930.26870.0540.109742.431467.19175.1834
174.3256-0.0639-2.33632.717-0.3056.4823-0.0807-0.2383-0.11110.2588-0.05180.1632-0.00380.11590.13260.4198-0.07770.00830.15330.00870.035845.081658.792422.2907
185.6537-3.3919-6.80553.37992.53999.97270.05290.2607-0.06430.1028-0.150.0482-0.16-0.31210.09710.3978-0.11560.040.19910.03530.064444.028657.2647-12.0965
190.5574-0.6542-0.41923.48081.96414.05140.00770.1813-0.0931-0.3266-0.16620.0431-0.01140.04650.15850.3224-0.10070.02150.43250.08070.059143.261942.8411-47.7541
200.2015-0.6535-0.25372.46451.7893.08330.08540.09050.0212-0.07-0.1387-0.03150.34990.33570.05330.4536-0.06970.05330.43880.07220.026746.944527.4579-34.9692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D3 - 219
5X-RAY DIFFRACTION5E3 - 256
6X-RAY DIFFRACTION6F1 - 276
7X-RAY DIFFRACTION7G0 - 99
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9I3 - 219
10X-RAY DIFFRACTION10J3 - 256
11X-RAY DIFFRACTION11K1 - 274
12X-RAY DIFFRACTION12L0 - 99
13X-RAY DIFFRACTION13M1 - 9
14X-RAY DIFFRACTION14N3 - 217
15X-RAY DIFFRACTION15O3 - 254
16X-RAY DIFFRACTION16P1 - 275
17X-RAY DIFFRACTION17Q0 - 99
18X-RAY DIFFRACTION18R1 - 9
19X-RAY DIFFRACTION19S3 - 217
20X-RAY DIFFRACTION20T2 - 256

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