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- PDB-1e3f: Structure of human transthyretin complexed with bromophenols: a n... -

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Basic information

Entry
Database: PDB / ID: 1e3f
TitleStructure of human transthyretin complexed with bromophenols: a new mode of binding
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT(THYROXINE) / ENVIRONMENTAL POLLUTANTS / BROMOPHENOLS
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGhosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of Human Transthyretin Complexed with Bromophenols : A New Mode of Binding
Authors: Ghosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N.
#1: Journal: The Design of Drugs to Macromolecular Targets / Year: 1992
Title: Multiple Modes of Binding of Thyroid Hormones and Other Iodothyronines to Human Plasma Transthyretin
Authors: De La Paz, P. / Burridge, J.M. / Oatley, S.J. / Blake, C.C.F.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: Structure of Prealbumin.Secondary,Tertiary and Quaternary Interactions Determined by Fourier Refinemrnt and Thyroxine Binding
Authors: Blake, C.C.F. / Geisow, M.J. / Oatley, S.J. / Rerat, C. / Rerat, B.
#3: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin : A Model of the Thyroid Hormone Nuclear Receptor
Authors: Blake, C.C.F. / Oatley, S.J.
History
DepositionJun 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)27,5552
Polymers27,5552
Non-polymers00
Water1,40578
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,1094
Polymers55,1094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.700, 85.400, 64.200
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-2043-

HOH

21B-2029-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9898, -0.1422, 0.0087), (-0.1423, 0.9898, -0.0059), (-0.0078, -0.0071, -0.9999)
Vector: 84.615, 5.956, 32.531)

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Components

#1: Protein TRANSTHYRETIN / / PREALBUMIN


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: PLASMA / References: UniProt: P02766
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
Temperature: 295 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.37 mMTTR1drop
2100 mMTris1drop
3100 mM1dropNaCl
41 mMEDTA1drop
550-55 %ammonium sulfate1reservoir
6100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 16505 / % possible obs: 85.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.228 / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 215400
Reflection shell
*PLUS
% possible obs: 88.7 % / Num. unique obs: 2102

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TTA

1tta


Resolution: 1.9→20 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1-9 OF BOTH CHAINS, AS WELL AS 126-127 OF CHAIN A AND 125-127 OF CHAIN B ARE ILL-DEFINED IN THE ELECTRON DENSITY MAPS AND HAVE BEEN OMITTED. THERE ARE SEVERAL OTHER RESIDUES WHERE ...Details: RESIDUES 1-9 OF BOTH CHAINS, AS WELL AS 126-127 OF CHAIN A AND 125-127 OF CHAIN B ARE ILL-DEFINED IN THE ELECTRON DENSITY MAPS AND HAVE BEEN OMITTED. THERE ARE SEVERAL OTHER RESIDUES WHERE THE MAIN CHAIN WAS VISIBLE BUT THE SIDE CHAIN DENSITIES WERE POOR. THESE RESIDUES HAVE BEEN REPLACED BY ALANINES. THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC DIAD PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM, I. E. XPRIME=-X, YPRIME= -Y, ZPRIME= Z. THERE ARE WATER MOLECULES LOCATED ON THE TWO- FOLD SYMMETRY AXIS (W47, W87) WHICH ARE ASSIGNED 50% OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 828 5 %RANDOM
Rwork0.193 ---
obs0.193 16447 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 0 78 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→2.05 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.309 153 5 %
Rwork0.259 3163 -
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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