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- PDB-1sn5: Crystal Structure of Sea Bream Transthyretin in complex with Trii... -

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Basic information

Entry
Database: PDB / ID: 1sn5
TitleCrystal Structure of Sea Bream Transthyretin in complex with Triiodothyronine at 1.90A Resolution
Componentstransthyretin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


thyroid hormone binding / hormone activity / extracellular region
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,5,3'TRIIODOTHYRONINE / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsEneqvist, T. / Lundberg, E. / Karlsson, A. / Huang, S. / Cantos, C.R. / Power, D.M. / Sauer-Eriksson, A.E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: High resolution crystal structures of piscine transthyretin reveal different binding modes for triiodothyronine and thyroxine.
Authors: Eneqvist, T. / Lundberg, E. / Karlsson, A. / Huang, S. / Santos, C.R. / Power, D.M. / Sauer-Eriksson, A.E.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transthyretin
B: transthyretin
C: transthyretin
D: transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5087
Polymers56,1104
Non-polymers1,3983
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-61 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.284, 58.284, 138.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
transthyretin /


Mass: 14027.579 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sparus aurata (gilthead seabream) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTT3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE / Triiodothyronine


Mass: 650.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12I3NO4 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 1550 MME, sodium citrate, ammonium sulphate, nickel sulphate, crystals were soaked in triiodothyronine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 36032 / Num. obs: 36032 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.434 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→19.76 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.858 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21081 3405 9.9 %RANDOM
Rwork0.1729 ---
all0.1765 36032 --
obs0.17658 31100 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 51 336 3916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213746
X-RAY DIFFRACTIONr_bond_other_d0.0010.023222
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.965133
X-RAY DIFFRACTIONr_angle_other_deg0.86837501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0083459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35715578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024161
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02729
X-RAY DIFFRACTIONr_nbd_refined0.2130.3697
X-RAY DIFFRACTIONr_nbd_other0.2190.33170
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5401
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0790.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6070.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8081.52300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50823731
X-RAY DIFFRACTIONr_scbond_it1.81331446
X-RAY DIFFRACTIONr_scangle_it3.0184.51402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 229
Rwork0.213 2020
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3803-0.03590.20960.5690.27910.7836-0.0014-0.00210.0586-0.04950.0295-0.09070.00180.021-0.02810.14540.00180.00950.1161-0.00310.1257-47.4065-11.7553-18.6348
20.6281-0.0857-0.00960.6484-0.31430.5097-0.0028-0.01550.05440.06570.05550.07220.0112-0.0342-0.05270.148-0.00030.00880.11930.00540.1224-67.6437-12.2818-16.9522
30.5147-0.02230.01741.66730.10350.41950.0005-0.0162-0.0088-0.0520.0558-0.14680.0730.0363-0.05630.18310.0105-0.0240.088-0.00950.1126-46.3886-36.8183-16.2289
40.49630.0625-0.18651.7497-0.21980.57750.02890.0642-0.07140.03840.00410.1602-0.00330.0079-0.0330.1537-0.0013-0.0250.0881-0.01250.1302-66.267-37.8834-19.9087
5-32.10231.6801-1.97845.3091-0.2795-2.38820.368-0.3038-0.14090.008-0.16170.00420.0395-0.0649-0.20630.1709-0.00570.00320.2283-0.01210.0007-56.9227-24.6996-17.9005
6-472.0583202.2824-487.9283736.705494.9096-362.53490.6312-0.27141.3947-9.18727.00141.6165-3.3362-4.1791-7.63260.2084-0.0806-0.10140.2904-0.14770.2457-37.8908-18.3922-4.1379
70.356-0.02690.04950.473-0.0330.091-0.0148-0.00040.02150.02560.02200.01680.0004-0.00720.17590.0037-0.00260.1159-0.00420.1035-56.8855-20.3833-17.1343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 127
2X-RAY DIFFRACTION2B11 - 125
3X-RAY DIFFRACTION3C11 - 125
4X-RAY DIFFRACTION4D11 - 123
5X-RAY DIFFRACTION5C601
6X-RAY DIFFRACTION5D602
7X-RAY DIFFRACTION6A701
8X-RAY DIFFRACTION7A702 - 809
9X-RAY DIFFRACTION7C602 - 671
10X-RAY DIFFRACTION7B128 - 231
11X-RAY DIFFRACTION7D603 - 656

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