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- PDB-1z7j: Human transthyretin (also called prealbumin) complex with 3, 3',5... -

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Basic information

Entry
Database: PDB / ID: 1z7j
TitleHuman transthyretin (also called prealbumin) complex with 3, 3',5,5'-tetraiodothyroacetic acid (t4ac)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / ALBUMIN / TRANSPORT / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / TETRAIODOTHYROACETIC ACID / T4AC / PREALBUMIN
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / 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
3,3',5,5'-TETRAIODOTHYROACETIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsNeumann, P. / Wojtczak, A. / Cody, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Ligand binding at the transthyretin dimer-dimer interface: structure of the transthyretin-T4Ac complex at 2.2 Angstrom resolution.
Authors: Neumann, P. / Cody, V. / Wojtczak, A.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex
Authors: Wojtczak, A. / Luft, J.R. / Cody, V.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin
Authors: Wojtczak, A. / Luft, J. / Cody, V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structures of Human Transthyretin Complexed with Thyroxine at 2.0 A Resolution and 3',5'-Dinitro-N-Acetyl-L-Thyronine at 2.2 A Resolution
Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
History
DepositionMar 25, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJun 7, 2005ID: 1KED
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 23, 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 / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0504
Polymers27,5552
Non-polymers1,4962
Water1,54986
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1018
Polymers55,1094
Non-polymers2,9914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9310 Å2
ΔGint-30 kcal/mol
Surface area18970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.462, 85.858, 65.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-128-

T4A

21B-129-

T4A

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P02766
#2: Chemical ChemComp-T4A / 3,3',5,5'-TETRAIODOTHYROACETIC ACID


Mass: 747.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8I4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 48% ammonium sulfate, 0.l M phosphate buffer, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K

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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: Jan 22, 1999 / 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: 2.2→43.461 Å / Num. obs: 11346 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.45 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.0587 / Net I/σ(I): 15.2777
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 2.44 / % possible all: 73.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: DIMER GENERATED FROM PDB ENTRY 2ROX STRUCTURE WITH ONLY PROTEIN ATOMS FROM RESIDUES 10-125 INCLUDED

2rox


Resolution: 2.2→14.87 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THIS COORDINATE SET COMPRISES TWO MONOMERS OF HUMAN TTR DIMER (CHAINS A AND B). MULTIPLE CONFORMATIONS HAVE BEEN FOUND FOR 13 RESIDUES. FOUR LIGAND MOLECULES HAVE BEEN FOUND (3,3',5,5'- ...Details: THIS COORDINATE SET COMPRISES TWO MONOMERS OF HUMAN TTR DIMER (CHAINS A AND B). MULTIPLE CONFORMATIONS HAVE BEEN FOUND FOR 13 RESIDUES. FOUR LIGAND MOLECULES HAVE BEEN FOUND (3,3',5,5'-TETRAIODOTHYROACETIC ACID) IN BOTH THE FORWARD AND THE REVERSE ORIENTATION. THERE ARE 81 WATER MOLECULES INCLUDED IN THE MODEL. RESIDUES A1-A9 AND A126-A127 OF THE FIRST MONOMER AND RESIDUES B201-B207 AND B326-B327 FROM THE SECOND ARE ILL-DEFINED IN THE ELECTRON DENSITY MAPS WEIGHTED ML MAPS AND HAVE BEEN OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 953 9.3 %RANDOM
Rwork0.173 ---
obs0.173 10228 78.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.14 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 44 86 1937
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it6.372.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 81 8.8 %
Rwork0.21 832 -
obs--57.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLIG.TOP
X-RAY DIFFRACTION3LIG.PARAMWATER.TOP

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