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- PDB-2j8u: Large CDR3a loop alteration as a function of MHC mutation. -

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Basic information

Entry
Database: PDB / ID: 2j8u
TitleLarge CDR3a loop alteration as a function of MHC mutation.
Components
  • AHIII TCR ALPHA CHAIN
  • AHIII TCR BETA CHAIN
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • SELF-PEPTIDE P1049
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / MHC I / MEMBRANE / SECRETED / GLYCATION / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / IMMUNE RESPONSE / DISEASE MUTATION / IMUNOREGULATORY COMPLEX / CLASS I MHC-TCR CO-CRYSTAL
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / PD-1 signaling / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / T cell receptor complex ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / PD-1 signaling / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / signaling receptor activity / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / carbohydrate binding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium
Similarity search - Function
ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 ...ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 / 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
T-cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / T-cell receptor beta chain V region C5 / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Endoplasmic reticulum membrane protein complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsMiller, P.J. / Benhar, Y.P. / Biddison, W. / Collins, E.J.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Single MHC mutation eliminates enthalpy associated with T cell receptor binding.
Authors: Miller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J.
History
DepositionOct 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.3Dec 12, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: SELF-PEPTIDE P1049
E: AHIII TCR ALPHA CHAIN
F: AHIII TCR BETA CHAIN
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
J: SELF-PEPTIDE P1049
L: AHIII TCR ALPHA CHAIN
M: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)186,54410
Polymers186,54410
Non-polymers00
Water0
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: SELF-PEPTIDE P1049
E: AHIII TCR ALPHA CHAIN
F: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,2725
Polymers93,2725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-55.2 kcal/mol
Surface area38760 Å2
MethodPISA
2
H: HLA class I histocompatibility antigen, A-2 alpha chain
I: Beta-2-microglobulin
J: SELF-PEPTIDE P1049
L: AHIII TCR ALPHA CHAIN
M: AHIII TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,2725
Polymers93,2725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-57.1 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.422, 83.893, 122.273
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31796.098 Da / Num. of mol.: 2 / Fragment: ECTO-DOMAIN, RESIDUES 25-299 / Mutation: K66A
Source method: isolated from a genetically manipulated source
Details: MUTATION OF HLA-A2.1 AT POSITION 66 LYSINE TO ALANINE
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 / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HAS EXTRA METHIONINE DUE TO E. COLI EXPRESSION / Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIP / References: UniProt: P61769
#3: Protein/peptide SELF-PEPTIDE P1049


Mass: 1049.263 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: SELF-PEPTIDE RECOGNIZED BY AHIII T CELL CLONE WHEN PRESENTED BY HLA-A2.1
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NPA0*PLUS
#4: Protein AHIII TCR ALPHA CHAIN


Mass: 21656.322 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII 12.2 T CELL CLONE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P01849*PLUS
#5: Protein AHIII TCR BETA CHAIN


Mass: 26890.883 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII 12.2 T CELL CLONE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P04213*PLUS
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ALA ENGINEERED RESIDUE IN CHAIN H, LYS 90 TO ALA
Sequence detailsMUTANT K66A ADDITIONAL METHIONINE AT N TERMINUS DUE TO EXPRESSION IN E. COLI

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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: 2.45 Å3/Da / Density % sol: 29.86 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.0 M NACL 20% PEG 8000 MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→30 Å / Num. obs: 38683 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.88→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.3 / % possible all: 69

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LP9

1lp9


Resolution: 2.88→122.17 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / SU B: 52.965 / SU ML: 0.46 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES IN THE TCR ALPHA CHAINS E AND L 50- 59 ARE COMPLETELY DISORDERED IN THE STRUCTURE AND THUS THE COORDINATES HAVE AN OCCUPANCY OF 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2007 4.9 %RANDOM
Rwork0.268 ---
obs0.269 38683 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.68 Å2
2--1.02 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.88→122.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13128 0 0 0 13128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02113331
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.751.92918117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.10751597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08923.667660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.391152138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1991582
X-RAY DIFFRACTIONr_chiral_restr0.0490.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1370.24767
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2880.28777
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0571.58351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.104212959
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0835913
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1374.55158
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.403 83
Rwork0.366 1750
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)
13.10430.77290.5474.02670.8853.27140.0384-0.0145-0.0036-0.06060.0230.00880.0942-0.0739-0.0614-0.12820.01220.0175-0.03530.0408-0.125615.964-1.35320.277
22.42770.41870.53716.329-5.48159.07720.1368-0.4338-0.39940.1112-0.05960.0260.4333-0.3573-0.07720.17730.0708-0.03760.2777-0.02930.107912.617-2.354.852
34.8698-2.2984-2.32427.20336.18477.8681-0.14780.09710.00880.3904-0.11630.60270.341-0.71450.2642-0.07790.0021-0.07060.46060.1412-0.0074-1.0725.96239.205
48.3043-1.9663-3.0832.62950.30548.7473-0.0823-0.3858-0.08210.33550.03070.1177-0.32750.20450.0517-0.0985-0.0905-0.06770.01850.0371-0.036135.648-5.911-5.656
511.6346-3.03771.23579.9241-2.625311.2578-0.00010.87740.3737-0.2908-0.1824-0.4556-0.6406-0.060.1826-0.16130.0266-0.04960.6318-0.05890.058744.23-1.157-38.34
62.94510.0853-0.22958.1134-4.85028.6681-0.03710.16390.10310.27760.20830.0663-0.6055-0.4405-0.1713-0.09840.1388-0.09580.2268-0.053-0.058417.6216.304-9.416
72.8077-2.3496-0.36777.12542.78465.36970.11930.3869-0.0487-0.1205-0.20960.5259-0.18810.20090.0902-0.1915-0.0541-0.19270.55640.02180.171627.4211.358-39.304
84.08970.84680.32323.80480.6464.7167-0.059-0.0052-0.0238-0.0675-0.00380.0710.4196-0.18040.0629-0.11190.0030.0371-0.05840.0328-0.109216.13741.00925.198
92.18810.6332-0.38966.938-7.7313.59150.149-0.2917-0.30480.16390.0482-0.0270.4647-0.3701-0.1972-0.0010.0132-0.13430.2453-0.06690.034813.15639.77559.881
104.2262-0.8213-2.68135.79044.1629.6399-0.06270.22530.19520.16750.01630.52330.0026-0.55970.0465-0.22360.0289-0.07910.33630.1397-0.0167-0.73148.48344.316
118.9221-0.5706-3.94782.590.39038.2584-0.1055-0.1264-0.0960.2672-0.0330.164-0.19730.06820.1386-0.1328-0.035-0.07880.02450.0428-0.021535.88236.209-0.723
1210.0494-4.22841.1112.6809-2.639113.57980.19930.20250.5405-0.8267-0.2485-0.809-0.73080.64660.0492-0.12020.0091-0.01490.5221-0.02040.015944.8141.811-33.259
132.2580.0843-0.24097.8781-4.90838.3661-0.05280.03920.10770.14080.31820.0801-0.4963-0.9367-0.2655-0.14850.124-0.10250.322-0.033-0.027818.04948.654-4.438
143.1671-2.608-0.95617.33711.93435.23520.32630.4180.0724-0.2162-0.21940.4642-0.34340.1179-0.1069-0.0897-0.0004-0.21810.46770.02810.08928.05844.24-34.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION2A184 - 275
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4E0 - 116
5X-RAY DIFFRACTION5E117 - 198
6X-RAY DIFFRACTION6F1 - 117
7X-RAY DIFFRACTION7F118 - 245
8X-RAY DIFFRACTION8H1 - 183
9X-RAY DIFFRACTION9H184 - 275
10X-RAY DIFFRACTION10I0 - 99
11X-RAY DIFFRACTION11L0 - 116
12X-RAY DIFFRACTION12L117 - 198
13X-RAY DIFFRACTION13M1 - 117
14X-RAY DIFFRACTION14M118 - 245

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