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- PDB-2fbr: Human transthyretin (TTR) complexed with bivalant amyloid inhibit... -

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Basic information

Entry
Database: PDB / ID: 2fbr
TitleHuman transthyretin (TTR) complexed with bivalant amyloid inhibitor (4 carbon linker)
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / TTR / AMYLOID / TRANSTHYRETIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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
Chem-44C / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsPalaninathan, S.K. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Synthesis and characterization of potent bivalent amyloidosis inhibitors that bind prior to transthyretin tetramerization.
Authors: Green, N.S. / Palaninathan, S.K. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0523
Polymers27,5552
Non-polymers4981
Water3,261181
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1056
Polymers55,1094
Non-polymers9952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8520 Å2
ΔGint-45 kcal/mol
Surface area18760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.599, 84.355, 65.569
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-173-

44C

21A-173-

44C

31A-173-

44C

41A-252-

HOH

51A-256-

HOH

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-44C / 4'-(4-{4-[(2-CARBOXYPHENYL)AMINO]PHENOXY}BUTOXY)-1,1'-BIPHENYL-4-CARBOXYLIC ACID


Mass: 497.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: TTR bivalent inhibitor complexes of 1:1 stoichiometry resulting from coassembly at 5-7 mg/mL (95-133 microM in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate ...Details: TTR bivalent inhibitor complexes of 1:1 stoichiometry resulting from coassembly at 5-7 mg/mL (95-133 microM in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate equilibrated against 2 M ammonium sulfate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→42.26 Å / Num. all: 38794 / Num. obs: 38794 / % possible obs: 97.73 % / Observed criterion σ(F): 38794 / Observed criterion σ(I): 0
Reflection shellResolution: 1.46→1.498 Å / % possible all: 94

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMZ

1bmz


Resolution: 1.46→42.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.382 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22356 2062 5 %RANDOM
Rwork0.21005 ---
all0.21076 0 --
obs0.21076 38794 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.46→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 37 181 1988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211868
X-RAY DIFFRACTIONr_bond_other_d0.0140.021675
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9552549
X-RAY DIFFRACTIONr_angle_other_deg1.48833914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255227
X-RAY DIFFRACTIONr_chiral_restr0.1260.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022054
X-RAY DIFFRACTIONr_gen_planes_other0.010.02374
X-RAY DIFFRACTIONr_nbd_refined0.1980.2286
X-RAY DIFFRACTIONr_nbd_other0.2670.21829
X-RAY DIFFRACTIONr_nbtor_other0.0870.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.225
X-RAY DIFFRACTIONr_mcbond_it1.1961.51146
X-RAY DIFFRACTIONr_mcangle_it2.16721867
X-RAY DIFFRACTIONr_scbond_it3.013722
X-RAY DIFFRACTIONr_scangle_it4.8514.5682
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 135
Rwork0.28 2400

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