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- PDB-1ie4: RAT TRANSTHYRETIN COMPLEX WITH THYROXINE (T4) -

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Basic information

Entry
Database: PDB / ID: 1ie4
TitleRAT TRANSTHYRETIN COMPLEX WITH THYROXINE (T4)
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / TRANSPORT OF THYROID HORMONES / RAT TRANSTHYRETIN / PREALBUMIN / THYROXINE COMPLEX
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / 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',5'-TETRAIODO-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsWojtczak, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of rat transthyretin (rTTR) complex with thyroxine at 2.5 A resolution: first non-biased insight into thyroxine binding reveals different hormone orientation in two binding sites.
Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structures of Human Transthyretin Complexed with Thyroxine at 2.0 ? Resolution and 3',5'-Dinitro-N-acetyl-L-thyronine at 2.2 ? Resolution
Authors: Wojtczak, A. / Cody, V. / Luft, J. / Pangborn, W.
#2: Journal: ACTA BIOCHIM.POL. / Year: 1997
Title: Crystal Structure of Rat Transthyretin at 2.5 A Resolution: First Report on a Unique Tetrameric Structure.
Authors: Wojtczak, A.
History
DepositionApr 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)56,0106
Polymers54,4574
Non-polymers1,5542
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-42 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.526, 82.526, 161.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN / TTR / TBPA / ATTR


Mass: 13614.147 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THIS SEQUENCE OCCURS NATURALLY IN RAT; PURIFIED FROM NATURAL SOURCE (SERUM)
Source: (natural) Rattus norvegicus (Norway rat) / Cellular location: BLOOD SERUM / Tissue: BLOOD SERUM / References: UniProt: P02767
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.472 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium sulfate, acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 %ammonium sulfate1reservoir
20.1 Macetate1reservoirpH5.0
355-65 %ammonium sulfate1drop
40.1 Macetate1droppH5.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: Collimator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→82.5 Å / Num. all: 18890 / Num. obs: 18890 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1786 / % possible all: 82.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 82.5 Å / Num. obs: 16558 / % possible obs: 83.5 % / Num. measured all: 83761
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1GKE

1gke


Resolution: 2.5→12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 177534.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1174 7.1 %RANDOM
Rwork0.209 ---
obs0.209 16557 83.3 %-
all-18890 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.32 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-12 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 48 172 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.128
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d4.68
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it9.672
X-RAY DIFFRACTIONc_scangle_it9.242.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 124 6.5 %
Rwork0.343 1787 -
obs--59.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3TH4.PARAMTH4.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.117

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