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- PDB-1e4h: Structure of human transthyretin complexed with bromophenols: a n... -

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Basic information

Entry
Database: PDB / ID: 1e4h
TitleStructure of human transthyretin complexed with bromophenols: a new mode of binding
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / TRANSPORT(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
PENTABROMOPHENOL / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionJul 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2000Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7166
Polymers27,5552
Non-polymers1,1614
Water2,738152
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,43212
Polymers55,1094
Non-polymers2,3238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area9230 Å2
ΔGint-40.2 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.000, 85.400, 64.400
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-998-

PBR

21A-998-

PBR

31A-998-

PBR

41A-998-

PBR

51B-999-

PBR

61B-999-

PBR

71B-999-

PBR

81B-999-

PBR

91A-2077-

HOH

101B-2005-

HOH

111B-2067-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9931, -0.1173, 0.0082), (-0.1174, 0.9931, -0.0005), (-0.0081, -0.0014, -1)
Vector: 85.518, 4.836, 32.585)

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Components

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


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PBR / PENTABROMOPHENOL


Mass: 488.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6HBr5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
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
26.1 mMPBP1drop
3100 mMTris1drop
4100 mM1dropNaCl
51 mMEDTA1drop
650-55 %ammonium sulfate1reservoir
7100 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, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 22174 / % possible obs: 97.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.279 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 119292
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 2762

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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: PDB ENTRY 1TTA

1tta


Resolution: 1.8→20 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE PENTABROMOPHENOL MOLECULE IS LOCATED RIGHT ON THE CRYSTALLOGRAPHIC Z AXIS. HALF THE MOLECULE WAS INCLUDED IN THE REFINEMENT WHILE THE OTHER HALF WAS GENERATED BY THE SYMMETRY OPERATION. ...Details: THE PENTABROMOPHENOL MOLECULE IS LOCATED RIGHT ON THE CRYSTALLOGRAPHIC Z AXIS. HALF THE MOLECULE WAS INCLUDED IN THE REFINEMENT WHILE THE OTHER HALF WAS GENERATED BY THE SYMMETRY OPERATION. WATER MOLECULES W302, W28, W350 ALSO LOCATED ON THE SAME SYMMETRY AXIS WERE KEPT FIXED IN POSITION DURING THE REFINEMENT. THERE WAS NO OBSERVABLE DENSITY FOR THE RESIDUES 1-9, AS WELL AS FOR 126- 127 OF BOTH THE CHAINS. THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER CAN BE GENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ALONG Z THROUGH THE ORIGIN OF THE COORDINATE SYSTEM.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1133 5 %RANDOM
Rwork0.193 ---
obs0.193 22132 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 36 152 1948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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: 1.8→1.94 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.262 246 5 %
Rwork0.219 4138 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PBP_HALF.PARPBP_HALF.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
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_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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