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- PDB-1dvu: CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH DIBENZOF... -

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Basic information

Entry
Database: PDB / ID: 1dvu
TitleCRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH DIBENZOFURAN-4,6-DICARBOXYLIC ACID
ComponentsTRANSTHYRETIN
KeywordsHORMONE/GROWTH FACTOR / THYROXINE TRANSPORT / SIGNALING PROTEIN / HORMONE-GROWTH FACTOR COMPLEX
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
DIBENZOFURAN-4,6-DICARBOXYLIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKlabunde, T. / Petrassi, H.M. / Oza, V.B. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Rational design of potent human transthyretin amyloid disease inhibitors.
Authors: Klabunde, T. / Petrassi, H.M. / Oza, V.B. / Raman, P. / Kelly, J.W. / Sacchettini, J.C.
History
DepositionJan 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0983
Polymers26,8422
Non-polymers2561
Water91951
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1966
Polymers53,6844
Non-polymers5122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7300 Å2
ΔGint-38 kcal/mol
Surface area18580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.140, 86.000, 65.100
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
11B-125-

DBF

21B-125-

DBF

DetailsThe biological assembly is a tetramer constructed from the homodimer (chain A and B) and a symmetry mate generated by the two-fold crystallographic axis.

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Components

#1: Protein TRANSTHYRETIN / PREALBUMIN


Mass: 13420.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-DBF / DIBENZOFURAN-4,6-DICARBOXYLIC ACID


Mass: 256.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: potassium chloride, potassium phosphate, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mM1dropKCl
3100 mMphosphate1drop
41 Mammonium sulfate1drop
52 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 26953 / Num. obs: 26953 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.83 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.316 / % possible all: 89.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 157123
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The structure contains two inhibitor molecules that bind in each of the two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an ...Details: The structure contains two inhibitor molecules that bind in each of the two independent binding sites of the tetramer. Since the binding is along the 2-fold crystallographic axis, an occupancy of 0.5 corresponds to saturation of each of the binding sites.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1881 -randomly chosen subset of 10 % of the observed reflections
Rwork0.198 ---
all-19108 --
obs-18752 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 19 51 1841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.278
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.198 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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