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- PDB-2f53: Directed Evolution of Human T-cell Receptor CDR2 residues by phag... -

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Basic information

Entry
Database: PDB / ID: 2f53
TitleDirected Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without apparent cross-reactivity
Components
  • Beta-2-microglobulin
  • Cancer/testis antigen 1B
  • HLA class I histocompatibility antigen
  • T-cell Receptor, alpha chain
  • T-cell receptor, beta chain
KeywordsIMMUNE SYSTEM / T-cell Receptor / CDR2 / Phage Display / Mutant / High Affinity / NY-ESO-1
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / 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 ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / 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 / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / lumenal side of endoplasmic reticulum membrane / 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 / 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 / Downstream TCR signaling / 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 / adaptive immune response / 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 / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...CTAG/Pcc1 family / Transcription factor Pcc1 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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
T cell receptor alpha chain constant / 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: 2.1 Å
AuthorsRizkallah, P.J. / Jakobsen, B.K. / Dunn, S.M. / Sami, M.
CitationJournal: Protein Sci. / Year: 2006
Title: Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity.
Authors: Dunn, S.M. / Rizkallah, P.J. / Baston, E. / Mahon, T. / Cameron, B. / Moysey, R. / Gao, F. / Sami, M. / Boulter, J. / Li, Y. / Jakobsen, B.K.
History
DepositionNov 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Currently there is no aminoacid sequence database reference available for T cell receptor ...SEQUENCE Currently there is no aminoacid sequence database reference available for T cell receptor alpha and beta chains (entities 4 and 5)

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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
B: Beta-2-microglobulin
C: Cancer/testis antigen 1B
D: T-cell Receptor, alpha chain
E: T-cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,67210
Polymers93,2815
Non-polymers3915
Water13,115728
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-67 kcal/mol
Surface area37750 Å2
MethodPISA
2
D: T-cell Receptor, alpha chain
E: T-cell receptor, beta chain
hetero molecules

A: HLA class I histocompatibility antigen
B: Beta-2-microglobulin
C: Cancer/testis antigen 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,67210
Polymers93,2815
Non-polymers3915
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation2_645-x+1,y-1/2,-z1
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-56 kcal/mol
Surface area39220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.234, 53.972, 119.905
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 1
Fragment: Extracellular domains alpha 1, alpha2 and alpha3, residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEX078 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11853.319 Da / Num. of mol.: 1 / Fragment: Beta-2 Microglobulin, residues 21-119 / Mutation: K91C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEX050 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein T-cell Receptor, alpha chain


Mass: 21211.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PIZ8, UniProt: P01848*PLUS
#5: Protein T-cell receptor, beta chain


Mass: 27267.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cancer/testis antigen 1B / L antigen family member 2 / LAGE-2 protein / Autoimmunogenic cancer/testis antigen NY-ESO-1


Mass: 1094.347 Da / Num. of mol.: 1 / Fragment: residues 157-165 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)
References: UniProt: P78358

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Non-polymers , 3 types, 733 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM HEPES, 8.5% Iso-propanol, 17% PEG4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2004 / Details: Mirror + Monochromator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→37.85 Å / Num. obs: 64982 / % possible obs: 98.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.178 / Rsym value: 0.178 / Net I/σ(I): 3
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym value% possible all
2-2.119.10.592720.0107297.4
2.11-2.2410.80.988910.77198.2
2.24-2.3910.80.983710.60198.5
2.39-2.5810.81.878320.40498.8
2.58-2.8310.72.672430.26799
2.83-3.1610.73.765630.17999.3
3.16-3.6510.64.658340.1399.4
3.65-4.4710.55.749510.10599.5
4.47-6.3210.16.138550.09299.6
6.32-37.719.55.921700.09498.7

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Phasing

Phasing MRRfactor: 47.3 / Cor.coef. Fo:Fc: 46.5 / Cor.coef. Io to Ic: 46.1
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoRECCP4 5.0phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BNR

2bnr


Resolution: 2.1→37.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic + TLS / Cross valid method: R-free / ESU R: 0.197 / ESU R Free: 0.184 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2910 5.173 %Random
Rwork0.166 ---
all0.169 ---
obs0.169 56251 98.695 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20 Å2-0.327 Å2
2--0.847 Å20 Å2
3----0.997 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 25 728 7315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216785
X-RAY DIFFRACTIONr_bond_other_d0.0010.025810
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9349218
X-RAY DIFFRACTIONr_angle_other_deg1.284313554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9045817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.48123.819343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.503151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8411548
X-RAY DIFFRACTIONr_chiral_restr0.1150.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.027611
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021439
X-RAY DIFFRACTIONr_nbd_refined0.2120.31279
X-RAY DIFFRACTIONr_nbd_other0.2030.36015
X-RAY DIFFRACTIONr_nbtor_refined0.1880.53129
X-RAY DIFFRACTIONr_nbtor_other0.090.53812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5875
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1330.53
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.379
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.523
X-RAY DIFFRACTIONr_mcbond_it3.29324092
X-RAY DIFFRACTIONr_mcbond_other1.15821660
X-RAY DIFFRACTIONr_mcangle_it4.8136613
X-RAY DIFFRACTIONr_mcangle_other2.36335624
X-RAY DIFFRACTIONr_scbond_it7.10242830
X-RAY DIFFRACTIONr_scbond_other2.23244731
X-RAY DIFFRACTIONr_scangle_it9.9862602
X-RAY DIFFRACTIONr_scangle_other4.95567930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1550.272120.2083889418498.016
2.155-2.2140.2682070.1933763405497.928
2.214-2.2780.2612200.1913697398698.269
2.278-2.3480.2551920.1923591385198.234
2.348-2.4250.2741920.1913438368798.454
2.425-2.510.2661740.1853400362898.512
2.51-2.6050.2611690.1783310352798.639
2.605-2.7110.271700.1833150336098.81
2.711-2.8310.2261910.1763034325699.048
2.831-2.9690.2631300.172889304899.049
2.969-3.130.2191490.1692792296799.124
3.13-3.320.2341380.1622631279099.247
3.32-3.5490.2411330.1652446259899.269
3.549-3.8330.2191500.1542298247099.109
3.833-4.1980.1931300.142103224899.333
4.198-4.6930.1921000.1231941205699.27
4.693-5.4170.179920.1371726183299.236
5.417-6.6310.211680.1841465154299.416
6.631-9.3640.299540.1771151121299.422
9.364-118.6780.2390.18262769995.279
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)
10.8203-0.0019-0.64630.54710.1052.7022-0.04530.0884-0.0647-0.01060.0163-0.018-0.0418-0.28830.029-0.13460.00120.09450.0286-0.0157-0.042116.896-3.00240.646
22.98241.40233.06531.46452.0738.97910.3377-0.043-0.28290.35940.2752-0.18770.80530.3524-0.6129-0.06820.1322-0.00340.0884-0.0607-0.105214.469-9.90675.635
33.0010.3296-1.96392.81670.60143.60520.0821-0.1832-0.1159-0.096-0.23590.07610.0748-0.36280.1538-0.1637-0.03290.03950.0830.005-0.08925.93-21.27557.591
42.11380.53021.22661.0193-1.07132.85730.07450.1379-0.08980.0303-0.10990.123-0.289-0.27370.0353-0.0910.01390.08040.0539-0.0348-0.025618.8930.07832.555
52.46751.0575-0.64241.8898-0.94756.7683-0.28610.22310.16190.09920.2017-0.0332-1.1833-0.01450.08450.0907-0.03440.0012-0.09560.0019-0.142323.96315.45714.513
62.86851.55130.35863.84880.30817.41320.08750.18610.61930.0798-0.03970.4697-1.0069-0.5064-0.0478-0.04810.05970.15040.02940.04560.017423.81920.237-20.182
71.64560.3865-0.45772.5255-0.7594.4979-0.05980.4275-0.0153-0.31440.19150.2944-0.0009-1.0975-0.1317-0.0961-0.020.05270.3509-0.0318-0.05069.354-1.66911.419
82.50040.9189-0.06391.101-0.09963.47910.1310.11560.04850.0216-0.0393-0.06650.4075-0.3975-0.0917-0.0846-0.09050.08340.1195-0.0347-0.141620.1842.688-18.323
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1801 - 180
22AA185 - 274185 - 274
33BB0 - 991 - 100
44CC1 - 91 - 9
55DD1 - 1103 - 112
66DD115 - 191117 - 193
77EE1 - 1153 - 117
88EE118 - 241120 - 243

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