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- PDB-8bhd: N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 8bhd
TitleN-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)
ComponentsGlutamate--tRNA ligase
KeywordsRNA BINDING PROTEIN / aminoacyl-tRNA synthetase / tRNA / protein complex / Cell surface protein / multi-aminoacyl-tRNA synthetase complex (MARS-MSC) / GST-like domain / aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMP)
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
TERBIUM(III) ION / glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium berghei ANKA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.17 Å
AuthorsBenas, P. / Jaramillo Ponce, J.R. / Legrand, P. / Frugier, M. / Sauter, C.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 France
Agence Nationale de la Recherche (ANR)ANR 20-SFRI-0012 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 France
Citation
Journal: Protein Sci. / Year: 2023
Title: Solution X-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes.
Authors: Jaramillo Ponce, J.R. / Theobald-Dietrich, A. / Benas, P. / Paulus, C. / Sauter, C. / Frugier, M.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein.
Authors: Jaramillo Ponce, J.R. / Kapps, D. / Paulus, C. / Chicher, J. / Frugier, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004
Title: Coot: model-building tools for molecular graphics.
Authors: Paul Emsley / Kevin Cowtan /
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The Buccaneer software for automated model building. 1. Tracing protein chains.
Authors: Cowtan, K.
#6: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Recent developments in classical density modification.
Authors: Cowtan, K.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Multivariate phase combination improves automated crystallographic model building.
Authors: Skubak, P. / Waterreus, W.J. / Pannu, N.S.
#8: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Methods used in the structure determination of bovine mitochondrial F1 ATPase.
Authors: Abrahams, J.P. / Leslie, A.G.
#9: Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: REFMAC5 for the refinement of macromolecular crystal structures.
Authors: Murshudov, G.N. / Skubak, P. / Lebedev, A.A. / Pannu, N.S. / Steiner, R.A. / Nicholls, R.A. / Winn, M.D. / Long, F. / Vagin, A.A.
#10: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Substructure solution with SHELXD.
Authors: Schneider, T.R. / Sheldrick, G.M.
#11: Journal: Acta Crystallogr.,Sect.A / Year: 2008
Title: A short history of SHELX.
Authors: Sheldrick, G.M.
#12: Journal: Nat Commun / Year: 2013
Title: Automatic protein structure solution from weak X-ray data.
Authors: Skubak, P. / Pannu, N.S.
#13: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: XDS.
Authors: Kabsch, W.
#14: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Integration, scaling, space-group assignment and post-refinement.
Authors: Kabsch, W.
#15: Journal: J.Synchrotron Radiat. / Year: 2019
Title: MXCuBE2: the dawn of MXCuBE Collaboration.
Authors: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. ...Authors: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. / Svensson, O. / Rey-Bakaikoa, V. / Chado, I. / Chavas, L.M.G. / Gadea, L. / Gourhant, P. / Isabet, T. / Legrand, P. / Savko, M. / Sirigu, S. / Shepard, W. / Thompson, A. / Mueller, U. / Nan, J. / Eguiraun, M. / Bolmsten, F. / Nardella, A. / Milan-Otero, A. / Thunnissen, M. / Hellmig, M. / Kastner, A. / Schmuckermaier, L. / Gerlach, M. / Feiler, C. / Weiss, M.S. / Bowler, M.W. / Gobbo, A. / Papp, G. / Sinoir, J. / McCarthy, A.A. / Karpics, I. / Nikolova, M. / Bourenkov, G. / Schneider, T. / Andreu, J. / Cuni, G. / Juanhuix, J. / Boer, R. / Fogh, R. / Keller, P. / Flensburg, C. / Paciorek, W. / Vonrhein, C. / Bricogne, G. / de Sanctis, D.
#16: Journal: Eur Phys J Plus / Year: 2017
Title: Status of the crystallography beamlines at synchrotron SOLEIL⋆
Authors: Coati, A. / Chavas, L.M.G. / Fontaine, P. / Foos, N. / Guimaraes, B. / Gourhant, P. / Legrand, P. / Itie, J.P. / Fertey, P. / Shepard, W. / Isabet, T. / Sirigu, S. / Solari, P.L. / Thiaudiere, D. / Thompson, A.
#17: Journal: Chem Sci / Year: 2017
Title: Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
Authors: Engilberge, S. / Riobe, F. / Di Pietro, S. / Lassalle, L. / Coquelle, N. / Arnaud, C.A. / Pitrat, D. / Mulatier, J.C. / Madern, D. / Breyton, C. / Maury, O. / Girard, E.
History
DepositionOct 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,58436
Polymers148,2395
Non-polymers4,34531
Water00
1
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
hetero molecules


  • defined by author
  • Evidence: gel filtration, performed on the native (without Tbxo4); see primary citation, light scattering, performed on the native (without Tbxo4); see primary citation, SAXS, performed on the native ...Evidence: gel filtration, performed on the native (without Tbxo4); see primary citation, light scattering, performed on the native (without Tbxo4); see primary citation, SAXS, performed on the native (without Tbxo4); see primary citation
  • 60.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)60,88114
Polymers59,2962
Non-polymers1,58512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56710
Polymers59,2962
Non-polymers1,2718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glutamate--tRNA ligase
hetero molecules

A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,27324
Polymers59,2962
Non-polymers2,97822
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
4
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,30131
Polymers118,5914
Non-polymers3,70927
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules

A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,72148
Polymers177,8876
Non-polymers5,83442
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)130.110, 88.510, 168.640
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-305-

TB

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 35 or resid 46...
d_2ens_1(chain "B" and (resid 8 through 35 or resid 46 through 66 or resid 83 through 224))
d_3ens_1(chain "C" and (resid 8 through 35 or resid 46 through 66 or resid 83 through 224))
d_4ens_1(chain "D" and (resid 8 through 35 or resid 46 through 107 or resid 116 through 224))
d_5ens_1(chain "E" and (resid 8 through 35 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILETHRA3 - 30
d_12ens_1GLUVALA33 - 53
d_13ens_1SERTHRA55 - 79
d_14ens_1ASNVALA81 - 189
d_21ens_1ILETHRB3 - 30
d_22ens_1GLUVALB38 - 58
d_23ens_1SERVALB60 - 193
d_31ens_1ILETHRC2 - 29
d_32ens_1GLUVALC31 - 51
d_33ens_1SERVALC53 - 186
d_41ens_1ILETHRD1 - 28
d_42ens_1GLUTHRD32 - 77
d_43ens_1ASNVALD79 - 187
d_51ens_1ILETHRE1 - 28
d_52ens_1GLUVALE31 - 51
d_53ens_1SERTHRE53 - 77
d_54ens_1ASNVALE79 - 187

NCS oper:
IDCodeMatrixVector
1given(0.3860195916, 0.900858052546, -0.198604239793), (-0.901993571174, 0.323459943276, -0.285974234252), (-0.193381675609, 0.289531404615, 0.93743004714)-7.64192847848, 102.109678547, -18.8084237145
2given(-0.384447720401, 0.902461327759, 0.194328336015), (0.900784758299, 0.320676522474, 0.292836792686), (0.201957345733, 0.287628440586, -0.93620676705)-7.05066015908, -20.9715850127, 116.751804179
3given(-0.688949698332, 0.578541066327, -0.436621744468), (-0.560255662749, -0.807255557296, -0.185612654668), (-0.459849872813, 0.116742022377, 0.880289381218)63.8308629298, 74.618217958, -34.5667585422
4given(0.690610836496, 0.575693295606, 0.437760096295), (0.556353321405, -0.809625007744, 0.187024941109), (0.462090526061, 0.114387832527, -0.879424680967)-65.5672672134, -2.79598319305, 69.6896780929

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Components

#1: Protein
Glutamate--tRNA ligase


Mass: 29647.863 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Plasmodium berghei Glu-RS with an insertion at position 2 (G2): cloning artifact. Residues I229 to S242 are degenerated from the original genetic sequence as a result of a cloning artifact ...Details: Plasmodium berghei Glu-RS with an insertion at position 2 (G2): cloning artifact. Residues I229 to S242 are degenerated from the original genetic sequence as a result of a cloning artifact and are followed by a His(6)-tag for purification purposes.
Source: (gene. exp.) Plasmodium berghei ANKA (eukaryote) / Strain: Anka / Gene: PBANKA_1362000 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A509AR09, glutamate-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Tb
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.12 %
Description: Crystals with a high solvent content that have required seeding in order to obtain an acceptable resolution.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use ...Details: Stock protein concentration: 6-9 mg/mL Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol Mix: 400 nL protein solution/seeds + 400 nL well solution Use of microseeding technique to improve crystal size. 1 microliter of a 100 mM Tbxo4 solution (ligand code 7MT) was added to the crystallization drop for a soacking of 1-2 minutes before freezing the crystals.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.631371 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020 / Details: Kirkpatrick-Baez bimorphic mirrors
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.631371 Å / Relative weight: 1
ReflectionResolution: 3.17→47.85 Å / Num. obs: 61436 / % possible obs: 99.83 % / Redundancy: 21.2 % / Biso Wilson estimate: 129 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1229 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.1259 / Net I/σ(I): 14.87
Reflection shellResolution: 3.17→3.283 Å / Redundancy: 19.8 % / Rmerge(I) obs: 2.335 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 6200 / CC1/2: 0.789 / Rpim(I) all: 0.5287 / Rrim(I) all: 2.395 / % possible all: 99.47

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Processing

Software
NameVersionClassification
PHENIXdev_4701refinement
CRANK2phasing
XSCALEdata scaling
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: SAD / Resolution: 3.17→47.85 Å / SU ML: 0.4742 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 3073 5.01 %
Rwork0.192 58286 -
obs0.1942 61359 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 169.93 Å2
Refinement stepCycle: LAST / Resolution: 3.17→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 0 71 0 8196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038355
X-RAY DIFFRACTIONf_angle_d0.583211285
X-RAY DIFFRACTIONf_chiral_restr0.04731253
X-RAY DIFFRACTIONf_plane_restr0.00411382
X-RAY DIFFRACTIONf_dihedral_angle_d11.88893029
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.786938003489
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.876337916278
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.97296313749
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.09860076341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.220.38761380.37592594X-RAY DIFFRACTION99.38
3.22-3.270.36611430.35122696X-RAY DIFFRACTION99.58
3.27-3.330.31181400.29692588X-RAY DIFFRACTION99.74
3.33-3.390.26691420.26272717X-RAY DIFFRACTION100
3.39-3.450.27431380.25492624X-RAY DIFFRACTION99.96
3.45-3.520.26621390.25472662X-RAY DIFFRACTION99.93
3.53-3.60.3221430.26562657X-RAY DIFFRACTION99.89
3.6-3.690.34021350.22162623X-RAY DIFFRACTION99.89
3.69-3.780.26781410.20732671X-RAY DIFFRACTION99.96
3.78-3.880.22541400.18632629X-RAY DIFFRACTION99.93
3.88-3.990.20021400.17192650X-RAY DIFFRACTION99.82
3.99-4.120.2251430.17742675X-RAY DIFFRACTION100
4.12-4.270.20421370.1722594X-RAY DIFFRACTION100
4.27-4.440.25281440.17652700X-RAY DIFFRACTION99.96
4.44-4.640.20581430.15982690X-RAY DIFFRACTION99.96
4.64-4.890.21041350.15862636X-RAY DIFFRACTION99.93
4.89-5.190.22121350.17742636X-RAY DIFFRACTION99.93
5.19-5.590.25151440.19092652X-RAY DIFFRACTION99.93
5.59-6.150.20521360.20972642X-RAY DIFFRACTION100
6.16-7.040.27331390.23652668X-RAY DIFFRACTION100
7.04-8.860.24931380.18932652X-RAY DIFFRACTION100
8.87-47.850.21011400.16092630X-RAY DIFFRACTION99.32
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)
16.458962195440.8300155714450.3660248254142.037716098352.130813843794.852675980450.540309240145-0.663105010188-0.3240110220730.231550055484-0.450807432848-0.5073085158910.1441031402980.613583878226-0.1166589310461.07970526611-0.0575463462367-0.07606610160381.099458414830.1354425537721.2805946111845.788648856323.783930812196.6737721371
23.66988592565-0.689604384849-0.2831618050640.831050897992.260282958284.914034649270.5341936298050.119577437307-1.13655016318-0.757268113920.03654354514550.8363119010090.154694656084-0.355242353331-0.5400752538730.772590377483-0.01814861911990.02775266853720.9511866039930.03466673701721.2419603784833.899864104322.457367431782.2498156325
36.15879213428-1.683061666430.005399357489714.56302818188-1.220871111252.42839647205-0.00614827087376-0.839428727390.6108096235970.303685249901-0.1119167202980.150757048881-0.46813045226-0.02959840760930.01208289182871.10476351328-0.1163389067130.09926316836311.10484107606-0.02725974429291.2612184312626.881758635933.009173029295.4050183226
43.55375213949-1.4787709411.319123246535.954017455111.678307455466.594026868280.149258013729-0.805187926341-0.2673153914490.310286952306-0.1866899898320.7899366384670.384163202068-0.859152402754-0.03438882174491.05081460495-0.05758628597530.06517223132141.297022478610.02795606396161.406059756617.3392028423242.262475573972.3564175646
55.179571354431.702986982310.3532531189895.105153119460.4357709139355.09352488362-0.9279190770082.215062741340.121825107174-1.065346317390.6048463107810.4564926282730.3926550835760.6996691758880.4357790024211.092048520620.052489148542-0.1902812543791.01426473036-0.01894033694071.2831126655110.33469914737.31089306671.5493522107
63.46100074615-0.8974605233490.3237288258414.146920178350.5417664034091.238516313320.2993522006650.1269622360110.0528268519733-0.30697316484-0.1543224416960.4548765822580.123082234862-0.15163778667-0.1609692979911.29106086180.137658109571-0.09628564484691.17176872869-0.02002088371411.3630387205111.762997171843.800583142762.722580539
72.757802063192.60670895898-0.04944052479194.951359443362.722371745775.2901536222-0.2731468138120.0382789004170.762506260823-0.3553972975280.366616097005-0.671527941833-0.1158899464931.12196038193-0.06516897317021.107745189820.1911384033750.006574590211941.09104093272-0.005380266207141.7407968154917.15679031562.443068430864.1396469484
82.20401663157-2.68131710724-0.4823477714068.155913200070.3043363915783.53402842596-0.383276321571-0.4193645646150.482640239890.8446423498630.317895604539-0.480006485559-0.3689968349060.08776685331130.07779951259220.9787395378630.115522257920.1251116577341.20126826738-0.1177466390171.3218570489111.340612329559.779549305676.5539504722
96.03572295875-2.20908935527-0.829288689487.483186037310.4737149015185.669761491960.4875521475111.638434025450.118980322986-1.539085243860.250695296720.415646194256-0.4276773964590.109739221624-0.5907165691051.668378058040.4915902398490.0626115561081.677654685110.3054324428311.3384294950416.086436864253.500600164838.6202284225
103.486077285164.26667955333.306416530694.611949008213.380359103355.01797443644-0.033576948841-2.207160374930.271037026022-0.881650548331-0.6888747686020.0601552822553-1.17575315437-1.066201607060.5049562780391.43312016020.1069474839640.06020355930881.743606553850.140981305631.7653648814217.056261365560.869052896840.8994975503
115.242082495930.881797805396-0.8272122345083.26352626134-1.168752485212.821958495520.7183275181580.821755218164-0.312936215566-0.0141038080113-0.2112279437620.09327161396460.100709656497-0.0291543941009-0.5286872384391.397497163080.3672918311150.03278904326311.455300014460.1410624592391.3683230592813.34189907152.274780031848.512062331
129.626302544534.27549283425-5.572188734923.31089681221-1.356552333013.49949460171.28685473403-1.38021470209-1.46916106559-0.515929101639-1.34574505326-0.3918629372480.3364395020090.6725992255180.09424580342021.165957608490.382668829429-0.04709320521951.19002461968-0.1642502417141.1558877341119.703181607940.711385948255.76608256
135.56937915778-0.75189555036-0.9894709734883.98039057618-0.394011069434.258130528991.4040263403-0.3421731076890.551301786780.514560767398-1.765495491650.976995889186-0.631290475120.2964613604550.2574959172421.186027641270.2259094817850.3013342381921.99280709656-0.02045934596621.5039375873436.29712024642.493365398752.1056983817
142.844394875771.33521613244-0.2605568997446.76581482732-0.7517689257356.328000235920.1374630556361.46431424764-0.818350513860.166884467231-0.0351875142558-0.6674694629551.810112891420.495049557076-0.04272078952051.813235043330.3941017496190.002158357040572.09203612280.167350127941.2015148047922.949943511732.099868247847.0913104353
154.75562656621-2.876517657370.3676613891773.621135035470.4837719800013.791330810140.5808328466780.6182095789331.30162400059-1.43821895725-0.0962370350347-1.601239519270.5009405867840.427348868634-0.6303408395651.449047318420.4167408148620.2361448085211.793850509980.0563137180881.2777869812333.070382754940.390735001540.6335818476
164.469767148544.740121819443.308028376959.64578947921.853926727482.712321667030.183321405344-0.518881197407-0.80395261561-1.140457334020.12171382818-2.13325869098-1.12801745364-1.02869636927-0.19711739232.026785330010.5197466033970.4612442062551.793889956560.06011760911721.2329012881226.409064989150.860718285833.0629582197
174.32934788580.7441506535121.081999473280.947307226047-0.06934162977891.49062024749-0.107769521426-0.493495510348-0.1014607392660.7604792907860.3942140088540.1551581989611.11069512707-0.548512421296-0.2793893807022.5063107616-0.0356050556465-0.1711224513012.12356158418-0.03722986898741.924213297714.2069919925312.29714726632.6968246572
186.92220813160.5714446709730.2892015188112.540776267930.159282632684.408652555240.7550321703362.13137023670.306571471514-0.449047062562-0.7889248556830.1111820501231.41187860034-0.021089005244-0.08918847524521.983314776940.29260546718-0.3040002260271.98013254297-0.2608889348671.5032260406717.507769561222.245503568124.9901815314
192.43280721108-0.713050353710.2554449922524.771278672630.8936318811964.799392279420.0936703963505-0.0136072472882-0.850559900728-0.4859014669220.162188508522-0.9300941652780.582022855115-0.486560160446-0.1710109834192.338882373680.375391723589-0.3536509358081.82263304858-0.03224534355951.6492044752830.603383021211.533619722434.8009939745
204.302053865620.463732930630.1282467994441.73113428436-0.4744891153590.5878250875071.321491760480.899096654861-0.2635551162270.23931801662-0.951969830063-0.7188194258760.6231569681851.10582135746-0.4141787079312.347885521620.456087752605-0.1510922097681.85216095124-0.06967647865391.2370892788923.952442548917.898214258541.5025783921
212.214825322591.105858142020.3701363361990.8195226051070.2609611107360.0209998588688-0.374572643976-0.505617969982-0.776267779758-1.16017551715-0.634999703475-0.391859345353.568886279610.3469920905750.7804737877673.15787456923-0.1953894519150.2373408870472.261927483130.1210945387011.080048124639.4429497259512.951307745445.8493981742
228.95514630281-0.02524044537014.205964139881.264873099321.966403541836.339408460552.718222130992.25140686289-2.54219210872-2.016967506990.355931558097-2.255738429141.382089562972.29537568875-1.479266266322.062084610550.2607223667450.3051783545423.64536775853-0.4935621087161.3142845540428.289595843217.57377259857.88242327094
233.036452024773.74451382859-0.7187225105614.61014117668-0.01867043311986.501748626610.1361751986381.39266795429-0.5988493290810.05325480606090.0879661633786-0.1061787356482.923966336291.73332524017-0.575010890662.56772054007-0.0845188317129-0.2985051581592.09352668376-0.3740133521741.5395923447514.659988496623.08736773952.08027125169
242.8512692213.15305251986-1.534582293884.347824964250.1641432105084.53008908322-1.21810240951.227220050750.950382290673-0.6988232820560.6156781833970.701620284329-0.1562187437210.5873723460310.1928799258262.21410732161-0.305853688582-0.005804780870792.770096602410.2397208551961.7657999695418.9447251229.3383341923.55746566071
256.27831583781-2.39227746027-1.86927016231.273500441041.834945766994.356847116792.598974042790.0951233104865-1.29037943017-0.838026747363-2.11348990640.674637327015-1.07348741252-0.644104898926-0.4561814663492.653578525960.430258571958-0.09149288027422.63065480025-0.4992585266981.8864230432132.063345388115.882221483511.8768371714
262.81532762416-0.755496445687-1.335612465151.396098138680.6491629265521.951782211771.034821521540.54764369432-0.128619976513-0.917906691933-0.387994986630.725504832471.07613873074-0.259519937768-0.6511096288562.334190652950.216001918481-0.4166550756761.87631740485-0.1012002292111.4753261413411.64107377416.310081970715.4615419901
279.59362845335-0.4608176684970.75037608977.684994667920.3700585438855.48777882581-2.69893153676-2.82304233432-0.92520108089-1.580280828761.73263973996-0.0129057615376-3.497739940780.2201119074651.096370311292.677898006010.220992675041-0.1672083559581.657281309750.08886419273151.4323615093614.015837246-3.86455808319.75334774527
280.6631254029661.42810138113-0.2195995878012.81369425937-0.5101770597610.1046546994410.0805271532614-1.81340748448-1.170371946180.766813949419-0.5943715609740.5334177440142.270617907560.6238935741560.3304460764573.25445622572-0.050053149415-0.224976216982.11438415867-0.008442793428341.612128910351.590361489838.344184497927.09844617968
290.135404308729-0.158629042430.3133966936430.785447186552-0.417565946311.18832019579-0.7500542038550.06662652887350.4226882816291.043358713391.35489303971-2.07094977147-1.176188260240.123189035546-0.3821345836392.743628217260.333682568157-0.4300289956942.07016518594-0.4600258913131.7082845815316.36433236944.356857674422.2336166661
300.811862033901-0.732987473170.53912216430.579589883864-0.4733288579920.35486293336-0.180928572941-1.40775575906-0.3890739914181.40489209975-0.131339058594-0.2083290593740.394570076709-1.750414428570.4898114489065.389641794020.157689228711-1.688035352081.8328666621-0.9558221060551.5914887794615.6025189857-7.14926479568-3.30018022948
313.91464366529-0.253464685933-0.1661618341932.200581263980.434276964510.192979830803-1.13581749730.4959197606060.155003122472-0.5532820763620.527503761208-1.373598223661.743114868991.837733715410.4684618031913.538264102980.315273365502-0.2518439546562.69490710967-0.2351923803580.62201428727314.69146985259.58240727465-3.35078420387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 99 )AA6 - 991 - 71
22chain 'A' and (resid 100 through 134 )AA100 - 13472 - 99
33chain 'A' and (resid 135 through 227 )AA135 - 227100 - 192
44chain 'B' and (resid 6 through 37 )BB6 - 371 - 32
55chain 'B' and (resid 38 through 60 )BB38 - 6033 - 52
66chain 'B' and (resid 61 through 116 )BB61 - 11653 - 85
77chain 'B' and (resid 117 through 155 )BB117 - 15586 - 124
88chain 'B' and (resid 156 through 227 )BB156 - 227125 - 196
99chain 'C' and (resid 7 through 34 )CC7 - 341 - 28
1010chain 'C' and (resid 35 through 60 )CC35 - 6029 - 45
1111chain 'C' and (resid 61 through 116 )CC61 - 11646 - 78
1212chain 'C' and (resid 117 through 134 )CC117 - 13479 - 96
1313chain 'C' and (resid 135 through 153 )CC135 - 15397 - 115
1414chain 'C' and (resid 154 through 166 )CC154 - 166116 - 128
1515chain 'C' and (resid 167 through 207 )CC167 - 207129 - 169
1616chain 'C' and (resid 208 through 227 )CC208 - 227170 - 189
1717chain 'D' and (resid 8 through 99 )DD8 - 991 - 69
1818chain 'D' and (resid 100 through 134 )DD100 - 13470 - 97
1919chain 'D' and (resid 135 through 155 )DD135 - 15598 - 118
2020chain 'D' and (resid 156 through 207 )DD156 - 207119 - 170
2121chain 'D' and (resid 208 through 225 )DD208 - 225171 - 188
2222chain 'E' and (resid 8 through 17 )EE8 - 171 - 10
2323chain 'E' and (resid 18 through 34 )EE18 - 3411 - 27
2424chain 'E' and (resid 35 through 52 )EE35 - 5228 - 37
2525chain 'E' and (resid 53 through 64 )EE53 - 6438 - 49
2626chain 'E' and (resid 65 through 133 )EE65 - 13350 - 96
2727chain 'E' and (resid 134 through 155 )EE134 - 15597 - 118
2828chain 'E' and (resid 156 through 166 )EE156 - 166119 - 129
2929chain 'E' and (resid 167 through 184 )EE167 - 184130 - 147
3030chain 'E' and (resid 185 through 194 )EE185 - 194148 - 157
3131chain 'E' and (resid 195 through 224 )EE195 - 224158 - 187

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