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- PDB-7yz8: Triclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant) -

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Basic information

Entry
Database: PDB / ID: 7yz8
TitleTriclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant)
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / mRNA binding and stability
Function / homology
Function and homology information


regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability ...regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
THIOCYANATE ION / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.
Authors: Cazzanelli, G. / Dalle Vedove, A. / Spagnolli, G. / Terruzzi, L. / Colasurdo, E. / Boldrini, A. / Patsilinakos, A. / Sturlese, M. / Grottesi, A. / Biasini, E. / Provenzani, A. / Quattrone, A. / Lolli, G.
History
DepositionFeb 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
C: YTH domain-containing family protein 1
D: YTH domain-containing family protein 1
E: YTH domain-containing family protein 1
F: YTH domain-containing family protein 1
G: YTH domain-containing family protein 1
H: YTH domain-containing family protein 1
I: YTH domain-containing family protein 1
J: YTH domain-containing family protein 1
K: YTH domain-containing family protein 1
L: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,47524
Polymers277,77812
Non-polymers69712
Water5,459303
1
A: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.225, 92.571, 113.940
Angle α, β, γ (deg.)72.870, 79.050, 67.870
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
21(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
31(chain C and (resid 366 through 396 or resid 398 through 557))
41(chain D and (resid 366 through 396 or resid 398 through 557))
51(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
61(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
71(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
81(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
91(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
101(chain J and (resid 366 through 396 or resid 398 through 557))
111(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
121(chain L and (resid 366 through 396 or resid 398 through 557))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSER(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA366 - 3967 - 37
12SERSERTYRTYR(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA398 - 45839 - 99
13TRPTRPASNASN(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA470 - 557111 - 198
21PROPROSERSER(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB366 - 3967 - 37
22SERSERTYRTYR(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB398 - 45839 - 99
23TRPTRPASNASN(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB470 - 557111 - 198
31PROPROSERSER(chain C and (resid 366 through 396 or resid 398 through 557))CC366 - 3967 - 37
32SERSERASNASN(chain C and (resid 366 through 396 or resid 398 through 557))CC398 - 55739 - 198
41PROPROSERSER(chain D and (resid 366 through 396 or resid 398 through 557))DD366 - 3967 - 37
42SERSERASNASN(chain D and (resid 366 through 396 or resid 398 through 557))DD398 - 55739 - 198
51PROPROSERSER(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE366 - 3967 - 37
52SERSERTYRTYR(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE398 - 45839 - 99
53TRPTRPASNASN(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE470 - 557111 - 198
61PROPROSERSER(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF366 - 3967 - 37
62SERSERTYRTYR(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF398 - 45839 - 99
63TRPTRPASNASN(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF470 - 557111 - 198
71PROPROSERSER(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG366 - 3967 - 37
72SERSERTYRTYR(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG398 - 45839 - 99
73TRPTRPASNASN(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG470 - 557111 - 198
81PROPROSERSER(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH366 - 3967 - 37
82SERSERTYRTYR(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH398 - 45839 - 99
83TRPTRPASNASN(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH470 - 557111 - 198
91PROPROSERSER(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II366 - 3967 - 37
92SERSERTYRTYR(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II398 - 45839 - 99
93TRPTRPASNASN(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II470 - 557111 - 198
101PROPROSERSER(chain J and (resid 366 through 396 or resid 398 through 557))JJ366 - 3967 - 37
102SERSERASNASN(chain J and (resid 366 through 396 or resid 398 through 557))JJ398 - 55739 - 198
111PROPROSERSER(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK366 - 3967 - 37
112SERSERTYRTYR(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK398 - 45839 - 99
113TRPTRPASNASN(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK470 - 557111 - 198
121PROPROSERSER(chain L and (resid 366 through 396 or resid 398 through 557))LL366 - 3967 - 37
122SERSERASNASN(chain L and (resid 366 through 396 or resid 398 through 557))LL398 - 55739 - 198

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Components

#1: Protein
YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 23148.166 Da / Num. of mol.: 12 / Fragment: YTH domain (residues 361-559)
Mutation: First residue G derives from the expression tag: E544A/E545V/E546V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYJ9
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.42 % / Mosaicity: 0.09 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 6-12% PEG3350, 0.2 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9429 Å / Relative weight: 1
ReflectionResolution: 2.5→49.05 Å / Num. obs: 87250 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 11.2 / Num. measured all: 301916
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.543.50.5771564644710.8120.360.6831.697.8
13.46-49.052.90.02215095150.9930.0160.02832.491.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCI

4rci


Resolution: 2.5→48.095 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 4291 4.92 %
Rwork0.1843 82912 -
obs0.1872 87203 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.46 Å2 / Biso mean: 62.7219 Å2 / Biso min: 24.61 Å2
Refinement stepCycle: final / Resolution: 2.5→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18362 0 36 303 18701
Biso mean--87.57 50.82 -
Num. residues----2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118940
X-RAY DIFFRACTIONf_angle_d1.17325479
X-RAY DIFFRACTIONf_chiral_restr0.0642643
X-RAY DIFFRACTIONf_plane_restr0.0093256
X-RAY DIFFRACTIONf_dihedral_angle_d17.07111446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10932X-RAY DIFFRACTION13.727TORSIONAL
12B10932X-RAY DIFFRACTION13.727TORSIONAL
13C10932X-RAY DIFFRACTION13.727TORSIONAL
14D10932X-RAY DIFFRACTION13.727TORSIONAL
15E10932X-RAY DIFFRACTION13.727TORSIONAL
16F10932X-RAY DIFFRACTION13.727TORSIONAL
17G10932X-RAY DIFFRACTION13.727TORSIONAL
18H10932X-RAY DIFFRACTION13.727TORSIONAL
19I10932X-RAY DIFFRACTION13.727TORSIONAL
110J10932X-RAY DIFFRACTION13.727TORSIONAL
111K10932X-RAY DIFFRACTION13.727TORSIONAL
112L10932X-RAY DIFFRACTION13.727TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.38071530.2935275598
2.5284-2.55820.35321430.2766275698
2.5582-2.58930.33251740.2722269697
2.5893-2.62210.33141320.2686274698
2.6221-2.65660.35511420.2596275798
2.6566-2.6930.33261580.2562273198
2.693-2.73150.31091530.2408280198
2.7315-2.77220.29261470.2306271698
2.7722-2.81560.28741190.2329279098
2.8156-2.86170.30661460.2359274898
2.8617-2.91110.31121380.2451280198
2.9111-2.9640.34831370.2562277198
2.964-3.0210.30041360.2444275298
3.021-3.08260.31131490.2211278798
3.0826-3.14970.27981420.2176271798
3.1497-3.22290.30011490.2152281899
3.2229-3.30350.28671370.2094275898
3.3035-3.39280.25881270.2003276398
3.3928-3.49260.23131520.2004274199
3.4926-3.60530.26451310.1952278899
3.6053-3.73410.27071310.1842283299
3.7341-3.88350.25711460.1826275399
3.8835-4.06020.25361450.1634278599
4.0602-4.27410.19721400.1494276899
4.2741-4.54170.18171500.1377278599
4.5417-4.89210.17341490.1269272998
4.8921-5.38380.20561540.1364277199
5.3838-6.16150.18451420.1581279499
6.1615-7.75760.21711300.1735279599
7.7576-48.0950.18751390.1596270896
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)
14.29740.8341.8045.73341.69275.92190.0342-0.913-0.22780.6388-0.8022-0.3771.04340.09190.67340.6176-0.09980.07090.53710.18070.478524.49780.477367.2293
21.8059-0.83810.60050.91650.41322.22170.1394-0.28250.00460.2511-0.10720.18780.5284-0.0457-0.09750.5052-0.07940.04480.336-0.0030.409915.653-7.067649.6288
31.473-0.37890.8091.93470.21212.70870.00480.18730.1875-0.0588-0.1441-0.03450.0985-0.0390.0950.27610.00210.09060.310.02610.35717.31392.192646.5828
43.20051.01960.45830.7299-0.33790.64240.1224-0.20381.5191-0.0136-0.4764-0.8888-0.77010.96420.47240.7694-0.20080.04330.5947-0.00230.870618.944913.777347.5432
51.3478-0.56710.51991.0529-0.19841.799-0.12470.2629-0.2499-0.0394-0.0381-0.02220.66470.27910.07610.58070.02940.07850.3134-0.03570.472622.0042-11.195242.1113
65.8275-0.49352.22827.5033.14994.9491-0.1544-0.07750.0037-0.5129-0.18590.57390.49150.32840.08970.40290.00920.05580.38210.01490.420418.0473-4.150136.628
73.855-0.37660.97972.75630.19943.2887-0.1767-0.2882-0.44570.2255-0.0698-0.06820.9262-0.21270.20860.7844-0.04240.1510.29810.04640.502819.0237-15.108448.8607
81.04320.9184-0.12693.6988-0.3991.8809-0.15740.10750.06110.040.2862-0.03340.07040.038-0.1730.29680.046-0.00230.39650.0550.380635.774413.043156.1526
91.8795-0.0595-0.85594.37631.08132.474-0.0436-0.0234-0.1771-0.07350.0926-0.1213-0.06770.0749-0.06520.2564-0.0358-0.06850.35610.04360.3836.88830.228568.9165
100.6981-0.22370.21012.48570.33251.2467-0.0335-0.2154-0.10.61070.0628-0.40530.14670.18130.00440.35110.0003-0.07240.39880.06280.39436.116325.963876.9949
113.10110.44191.99944.8013-0.36143.42440.1405-0.8233-0.35740.9855-0.4158-0.4080.0708-0.07930.03420.43030.07450.06360.56130.11190.684456.255614.363544.2239
121.3431-0.78051.21542.02040.31013.0114-0.1109-0.0510.1639-0.3874-0.1414-0.44910.0480.24570.24810.33690.05610.10570.43790.10820.463641.570622.207730.603
132.45230.39840.84010.8115-0.14611.1350.0127-0.009-0.70090.26640.2807-0.3193-0.0275-0.1939-0.26620.43970.08680.08940.41150.07450.561541.22099.335438.6866
141.4043-1.00820.09852.29130.68383.0490.11390.2088-0.1271-0.3449-0.17020.177-0.2046-0.32350.06830.30420.02290.06140.5194-0.02810.488536.277115.508628.1733
152.4383-0.59230.31360.55761.05662.2749-0.1676-0.0123-0.2762-0.0139-0.12080.11970.0983-0.10670.23620.27760.01310.0680.48450.08940.509134.810619.982133.0841
162.2874-0.7723-0.58261.93771.13830.6751-0.0561-0.1270.176-0.6772-0.01631.24660.3184-0.63720.19560.31830.0180.01440.70340.03590.390728.390119.493829.3585
171.80230.12840.78291.5055-0.11332.96270.23740.3256-0.081-0.26890.0918-0.2936-0.34750.7216-0.06040.32560.02860.04740.50730.07730.509540.06830.176534.1228
181.87830.9903-0.59043.9061-0.99131.3515-0.1812-0.1442-0.51090.0110.1062-0.29340.54640.31920.01740.50130.1695-0.03120.49980.12750.6542.22281.744450.7038
192.28551.14610.57253.4383-0.16253.3592-0.3936-0.6579-0.22670.9396-0.19290.99760.545-0.80710.45770.7057-0.15440.25350.5893-0.1890.6581-0.295915.69679.9737
201.81340.38-0.65643.05420.62143.0144-0.027-0.32350.34280.2354-0.31940.0632-0.0327-0.14360.34880.3342-0.0785-0.00560.3418-0.01540.412110.329928.05479.5717
211.3069-0.6104-0.97562.82090.6763.4536-0.0444-0.01470.00470.0252-0.43150.3147-0.0891-0.17770.44440.2891-0.0818-0.0190.3774-0.05790.51535.228628.149472.2248
223.11780.64860.60881.09870.11681.50380.2774-0.00450.1660.5396-0.256-0.17440.78130.45610.04070.73990.0424-0.00570.48730.13430.562626.687512.006380.8477
231.5936-0.37311.05690.94740.19382.73020.25210.2143-0.6207-0.26340.48410.33950.475-1.5563-0.61080.6867-0.30380.00311.02360.03680.8172-12.5259-6.78820.884
241.8838-0.79061.67911.85570.0521.88830.05820.13580.1311-0.04660.1850.2194-0.3176-0.21430.31640.3402-0.04810.02010.44080.00590.422.75263.928423.3366
252.21550.5261.87090.30930.51281.8813-0.24070.0232-0.389-0.34670.25380.0124-0.1936-0.6637-0.0170.4045-0.0869-0.00860.8235-0.01910.49770.893-1.364713.0188
262.9405-1.42010.21942.11920.50032.22920.0718-0.0165-0.0042-0.06030.0383-0.16830.1947-0.1241-0.05510.2801-0.08380.02250.3617-0.03980.50642.7168-1.573425.9808
272.5556-1.410.17912.5956-0.54612.18930.25380.33060.0773-0.6038-0.0788-0.16550.2151-0.1866-0.22190.4252-0.06850.05820.5175-0.03950.52050.3146-2.129319.108
281.51280.59760.87021.42840.3761.530.0492-0.0003-0.01620.142-0.08340.1116-0.1429-0.47260.03280.26970.02810.04080.5871-0.01130.5264-5.25458.148930.9073
293.58340.5099-1.9841.41460.04132.84110.14130.67470.0016-0.45660.1969-0.0233-0.1518-0.7171-0.06440.6331-0.1353-0.07310.740.04360.47012.03841.8017-0.5958
300.6371-0.0532-0.02170.1499-0.14430.1269-0.12590.86640.5925-0.587-0.1622-0.682-0.40390.62060.05680.8445-0.20310.30540.8169-0.04930.987519.57571.116893.2051
310.7997-0.1419-0.19161.5736-0.37072.6911-0.0655-0.05540.40290.10840.0239-0.50110.11880.53180.10280.5197-0.0346-0.00630.5877-0.07890.523916.3313-10.5636110.5979
321.88080.3817-0.66570.5544-1.00861.8392-0.4357-0.09780.0394-0.2420.0431-0.4055-0.60670.24650.17250.6506-0.19120.04160.48080.00930.41397.88940.5453104.815
331.9492-0.21150.06263.09741.10333.3870.2034-0.38750.0530.09310.264-0.4326-0.47670.2421-0.45520.5388-0.15470.05240.5306-0.06450.479710.5666-6.1458115.6643
340.8472-0.21160.16762.6801-0.09742.9784-0.33360.07780.2476-0.14020.14110.7517-0.918-0.32280.06341.0668-0.01920.04120.5102-0.1650.66928.57775.2104114.4279
350.56670.61270.22811.5878-0.29912.1219-0.09750.0764-0.0678-0.07290.2047-0.16650.24070.1474-0.09950.4925-0.06620.04650.43-0.04090.355510.7349-17.5665110.1416
362.8467-1.82070.27484.06140.43870.61370.17340.08260.4185-0.4752-0.0835-0.2859-0.3484-0.08470.06670.9078-0.13320.1920.52570.02640.4581.1057.207694.352
371.8187-0.2611-0.96843.86340.29064.4684-0.0619-0.227-0.07170.13310.20880.1815-0.13530.1916-0.18850.42010.1480.03640.3937-0.02110.3925.0518-29.601731.1697
381.5935-0.7879-0.18641.86680.14212.4287-0.3424-0.4064-0.24760.43080.1815-0.3187-0.02680.13990.05860.45660.10880.0350.38430.00480.449827.3443-32.065432.1302
394.28120.5535-0.96563.52971.58712.583-0.4526-0.1129-0.0254-0.1212-0.08770.62881.26390.28210.50010.74030.0329-0.05590.4159-0.01880.651625.4724-45.648818.6566
401.6974-0.2775-0.37152.07870.09433.1077-0.21550.1669-0.51730.00230.01020.15090.4378-0.19290.24660.43640.0653-0.02970.4462-0.04150.593619.8878-39.620825.9856
413.52070.07340.8251.63810.36680.7315-0.08-0.8830.57350.64090.3824-0.07820.22570.6048-0.39310.94220.3964-0.11441.195-0.16030.562939.088-32.354249.2595
420.42570.7267-0.29571.2556-0.56261.00130.3959-0.15070.5366-0.07150.30880.1251-0.3146-0.13030.35861.8969-0.49970.8604-0.0802-0.02391.12061.0999-4.403180.7035
430.0295-0.04140.02213.11391.31710.55120.77130.11750.3187-0.5864-0.2435-1.6514-1.03340.57270.24631.5733-0.20880.52180.61520.16010.696410.2862-19.089668.5233
442.73570.0157-0.45963.26131.98353.55130.3932-0.1367-0.0593-0.4297-0.22680.0013-0.842-0.1616-0.15450.7611-0.08740.0130.36540.04010.3394-3.6025-25.481377.9034
453.0715-0.8184-0.53831.2716-0.81011.34830.86860.7736-0.1308-1.3757-0.6184-0.1487-1.778-0.44940.08811.53990.14830.18320.57420.05450.3018-1.7573-24.142563.0476
462.6882-0.1088-1.26470.3722-0.63182.44380.2519-0.06370.065-0.9079-0.2999-0.0151-0.488-0.22010.37361.40970.02630.12370.4258-0.10820.494-17.87-9.572586.311
471.4533-0.64440.86361.28790.37861.4482-0.13810.19150.0675-0.3250.02180.0175-0.41380.03190.08390.6166-0.1040.09050.55290.0430.448520.446419.38460.0526
481.1077-0.05661.36321.5283-0.9762.2670.14290.19970.0483-0.3116-0.3981-0.1902-0.11850.13020.16310.4621-0.0832-0.0470.6451-0.00440.492210.165317.11466.5449
492.9434-0.66010.00351.95650.83513.7089-0.3297-0.17-0.15190.1970.0836-0.1201-0.22160.0210.180.5156-0.01020.01840.39340.03730.408323.344819.706514.9252
500.97110.280.70511.84110.2971.3083-0.2992-0.2977-0.27710.23710.08390.19740.4738-0.47370.12280.4913-0.03420.04930.40370.02890.464415.325117.934710.4756
511.55180.30260.38611.68450.08541.7972-0.16620.2676-0.277-0.4780.1274-0.36210.27980.3645-0.01360.6094-0.08180.16290.5473-0.05530.540427.31698.94023.6114
522.5456-0.1211-1.1011.4204-0.81151.45-0.34110.46370.0019-0.03160.22480.5409-0.3624-0.3875-0.02490.6921-0.0429-0.15390.9724-0.04270.8981-3.444813.99453.6833
531.45140.2285-0.72992.09150.01633.3950.1482-0.17160.1797-0.3231-0.09410.1102-0.3526-0.0781-0.0260.72640.0360.02640.4202-0.05340.3803-19.18734.7794108.2845
542.3023-1.2236-0.55521.61510.69211.7890.0757-0.1063-0.0968-0.57080.05-0.1836-0.1276-0.0006-0.07610.9312-0.1280.11550.4155-0.00720.4657-2.9331-5.82691.3141
557.48560.3047-2.85842.3071-2.39183.9341-0.0479-0.0129-0.45930.31270.43910.53240.23510.35870.02890.75950.3917-0.08441.3261-0.08730.57719.894536.04850.18
561.53351.1767-0.36211.7223-0.65081.7317-0.27480.1845-0.6512-0.05030.458-1.21450.27570.4128-0.27180.57130.1799-0.09981.073-0.27420.811433.011745.39336.8619
572.10680.5327-0.89733.5992-0.05823.461-0.54330.39290.23010.17680.32550.1664-1.0475-0.74030.1880.54490.1855-0.13210.8131-0.05240.506117.393850.564230.0952
580.5413-0.2606-0.11751.0128-0.17491.8367-0.0943-0.67890.06250.64720.34520.3127-0.1610.1653-0.16970.68780.32310.00960.94870.03660.423512.370542.377637.7618
592.31520.5193-0.71983.46150.953.5279-0.2647-0.27020.3019-0.48920.5273-0.1151-0.07680.1516-0.21640.48570.1396-0.04690.4917-0.01160.311220.498644.473624.3057
600.3308-0.1004-0.47311.3120.02421.3857-0.5485-0.44740.0623-0.18030.25150.5933-0.0933-0.11170.30550.48610.2433-0.0520.7814-0.01630.612814.773243.361132.0939
610.96330.1468-0.01492.3170.13252.6381-0.2146-0.7440.455-0.02390.4836-0.2569-0.30270.4915-0.19730.51650.1866-0.12340.8832-0.22840.600824.727456.658833.9293
624.58151.01120.83781.4994-0.04121.1723-0.0201-0.30690.22850.42690.11670.21890.55160.3946-0.09080.80540.37540.04991.0190.01570.54661.517440.451446.4595
631.04450.0682-0.01492.1706-0.28421.79790.27330.19150.1753-0.1238-0.46780.9258-0.7548-0.49990.21270.94850.1729-0.19540.5923-0.23350.821235.9979-23.917381.2499
643.10621.94210.65673.3952-2.5184.44210.63570.6592-1.1688-1.0702-1.33070.4799-0.2219-0.4769-0.00960.60230.2202-0.44840.6879-0.41980.860542.3613-38.642273.9437
651.61341.056-0.45672.0258-0.10242.08380.55730.2267-0.3189-0.009-0.50620.8173-0.3761-0.23730.03460.73230.0949-0.29960.5141-0.23920.774738.4914-29.786583.8553
662.0089-0.19580.57513.8710.35572.30860.2997-0.04410.01550.0915-0.5790.6743-0.2354-0.21860.17690.67320.0017-0.09530.5625-0.21320.644940.1411-30.733488.2431
670.6735-0.54930.18650.5929-0.25140.9191-0.17850.70790.2774-0.6966-0.06830.03470.2004-0.18350.29271.58360.146-0.15880.6313-0.00380.714549.4626-9.07572.7155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 374 )A365 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 398 )A375 - 398
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 457 )A399 - 457
4X-RAY DIFFRACTION4chain 'A' and (resid 458 through 475 )A458 - 475
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 504 )A476 - 504
6X-RAY DIFFRACTION6chain 'A' and (resid 505 through 512 )A505 - 512
7X-RAY DIFFRACTION7chain 'A' and (resid 513 through 531 )A513 - 531
8X-RAY DIFFRACTION8chain 'A' and (resid 532 through 559 )A532 - 559
9X-RAY DIFFRACTION9chain 'B' and (resid 365 through 475 )B365 - 475
10X-RAY DIFFRACTION10chain 'B' and (resid 476 through 559 )B476 - 559
11X-RAY DIFFRACTION11chain 'C' and (resid 364 through 374 )C364 - 374
12X-RAY DIFFRACTION12chain 'C' and (resid 375 through 398 )C375 - 398
13X-RAY DIFFRACTION13chain 'C' and (resid 399 through 414 )C399 - 414
14X-RAY DIFFRACTION14chain 'C' and (resid 415 through 452 )C415 - 452
15X-RAY DIFFRACTION15chain 'C' and (resid 453 through 504 )C453 - 504
16X-RAY DIFFRACTION16chain 'C' and (resid 505 through 512 )C505 - 512
17X-RAY DIFFRACTION17chain 'C' and (resid 513 through 531 )C513 - 531
18X-RAY DIFFRACTION18chain 'C' and (resid 532 through 558 )C532 - 558
19X-RAY DIFFRACTION19chain 'D' and (resid 364 through 388 )D364 - 388
20X-RAY DIFFRACTION20chain 'D' and (resid 389 through 452 )D389 - 452
21X-RAY DIFFRACTION21chain 'D' and (resid 453 through 531 )D453 - 531
22X-RAY DIFFRACTION22chain 'D' and (resid 532 through 558 )D532 - 558
23X-RAY DIFFRACTION23chain 'E' and (resid 365 through 388 )E365 - 388
24X-RAY DIFFRACTION24chain 'E' and (resid 389 through 398 )E389 - 398
25X-RAY DIFFRACTION25chain 'E' and (resid 399 through 414 )E399 - 414
26X-RAY DIFFRACTION26chain 'E' and (resid 415 through 452 )E415 - 452
27X-RAY DIFFRACTION27chain 'E' and (resid 453 through 488 )E453 - 488
28X-RAY DIFFRACTION28chain 'E' and (resid 489 through 531 )E489 - 531
29X-RAY DIFFRACTION29chain 'E' and (resid 532 through 558 )E532 - 558
30X-RAY DIFFRACTION30chain 'F' and (resid 364 through 374 )F364 - 374
31X-RAY DIFFRACTION31chain 'F' and (resid 375 through 398 )F375 - 398
32X-RAY DIFFRACTION32chain 'F' and (resid 399 through 414 )F399 - 414
33X-RAY DIFFRACTION33chain 'F' and (resid 415 through 452 )F415 - 452
34X-RAY DIFFRACTION34chain 'F' and (resid 453 through 475 )F453 - 475
35X-RAY DIFFRACTION35chain 'F' and (resid 476 through 531 )F476 - 531
36X-RAY DIFFRACTION36chain 'F' and (resid 532 through 558 )F532 - 558
37X-RAY DIFFRACTION37chain 'G' and (resid 365 through 440 )G365 - 440
38X-RAY DIFFRACTION38chain 'G' and (resid 441 through 488 )G441 - 488
39X-RAY DIFFRACTION39chain 'G' and (resid 489 through 504 )G489 - 504
40X-RAY DIFFRACTION40chain 'G' and (resid 505 through 531 )G505 - 531
41X-RAY DIFFRACTION41chain 'G' and (resid 532 through 557 )G532 - 557
42X-RAY DIFFRACTION42chain 'H' and (resid 365 through 374 )H365 - 374
43X-RAY DIFFRACTION43chain 'H' and (resid 375 through 388 )H375 - 388
44X-RAY DIFFRACTION44chain 'H' and (resid 389 through 475 )H389 - 475
45X-RAY DIFFRACTION45chain 'H' and (resid 476 through 531 )H476 - 531
46X-RAY DIFFRACTION46chain 'H' and (resid 532 through 559 )H532 - 559
47X-RAY DIFFRACTION47chain 'I' and (resid 364 through 398 )I364 - 398
48X-RAY DIFFRACTION48chain 'I' and (resid 399 through 414 )I399 - 414
49X-RAY DIFFRACTION49chain 'I' and (resid 415 through 440 )I415 - 440
50X-RAY DIFFRACTION50chain 'I' and (resid 441 through 475 )I441 - 475
51X-RAY DIFFRACTION51chain 'I' and (resid 476 through 531 )I476 - 531
52X-RAY DIFFRACTION52chain 'I' and (resid 532 through 558 )I532 - 558
53X-RAY DIFFRACTION53chain 'J' and (resid 365 through 531 )J365 - 531
54X-RAY DIFFRACTION54chain 'J' and (resid 532 through 559 )J532 - 559
55X-RAY DIFFRACTION55chain 'K' and (resid 365 through 374 )K365 - 374
56X-RAY DIFFRACTION56chain 'K' and (resid 375 through 388 )K375 - 388
57X-RAY DIFFRACTION57chain 'K' and (resid 389 through 398 )K389 - 398
58X-RAY DIFFRACTION58chain 'K' and (resid 399 through 414 )K399 - 414
59X-RAY DIFFRACTION59chain 'K' and (resid 415 through 440 )K415 - 440
60X-RAY DIFFRACTION60chain 'K' and (resid 441 through 475 )K441 - 475
61X-RAY DIFFRACTION61chain 'K' and (resid 476 through 531 )K476 - 531
62X-RAY DIFFRACTION62chain 'K' and (resid 532 through 558 )K532 - 558
63X-RAY DIFFRACTION63chain 'L' and (resid 366 through 414 )L366 - 414
64X-RAY DIFFRACTION64chain 'L' and (resid 415 through 428 )L415 - 428
65X-RAY DIFFRACTION65chain 'L' and (resid 429 through 452 )L429 - 452
66X-RAY DIFFRACTION66chain 'L' and (resid 453 through 531 )L453 - 531
67X-RAY DIFFRACTION67chain 'L' and (resid 532 through 558 )L532 - 558

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