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- PDB-4tqi: Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylidenea... -

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Basic information

Entry
Database: PDB / ID: 4tqi
TitleHuman transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid in a dual binding mode
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / PEG TTR crystallization / Flourenone based amyloid antagonist and inhibitor / Prealbumin / Dual binding mode / hormone transporter
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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-6BD / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsStura, E.A. / Ciccone, L. / Nencetti, S. / Rossello, A. / Orlandini, E.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2015
Title: X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors.
Authors: Ciccone, L. / Nencetti, S. / Rossello, A. / Tepshi, L. / Stura, E.A. / Orlandini, E.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,3026
Polymers27,5552
Non-polymers7474
Water4,774265
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60312
Polymers55,1094
Non-polymers1,4948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)43.250, 86.370, 63.340
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-201-

6BD

21A-201-

6BD

31A-201-

6BD

41B-201-

6BD

51B-201-

6BD

61B-201-

6BD

71B-201-

6BD

81A-302-

HOH

91B-335-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


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-6BD / (2S)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methylpropanoic acid / (S)-3-(9H-fluoren-9-ylideneaminooxy)-2-methylpropanoic acid


Mass: 281.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: protein: TTR 10 mg/ml + ligand 0.66 milli-M in 0.1 M NaCl, 0.05 M Na acetate, pH 5.5. Precipitant: 70% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 30% (12% MPEG-5K, 0.1 M sodium ...Details: protein: TTR 10 mg/ml + ligand 0.66 milli-M in 0.1 M NaCl, 0.05 M Na acetate, pH 5.5. Precipitant: 70% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 30% (12% MPEG-5K, 0.1 M sodium acetate, pH 5.5). Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 10% PEG 10K, 0.1 M (mixed sodium propionate, sodium cacodylate, Bis-Tris-propane) (65% component A pH 4; 35% B pH 9.5)
PH range: 5.5 - 6.5 / Temp details: cooled inbubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2013
Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut Si[111] crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.25→43.2 Å / Num. obs: 63728 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 8.04 % / Rmerge(I) obs: 0.151 / Rsym value: 0.14 / Net I/σ(I): 11.11
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.64 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
MxCuBEdata collection
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GS0

3gs0


Resolution: 1.25→35.72 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3181 5 %Random
Rwork0.173 ---
obs0.174 63673 95.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 54 265 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062258
X-RAY DIFFRACTIONf_angle_d1.063118
X-RAY DIFFRACTIONf_dihedral_angle_d14.139801
X-RAY DIFFRACTIONf_chiral_restr0.044324
X-RAY DIFFRACTIONf_plane_restr0.006410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2489-1.26760.45591260.40962402X-RAY DIFFRACTION88
1.2676-1.28740.37461330.37242520X-RAY DIFFRACTION93
1.2874-1.30850.35131330.37932527X-RAY DIFFRACTION93
1.3085-1.3310.3781310.35022518X-RAY DIFFRACTION94
1.331-1.35520.35031360.3322582X-RAY DIFFRACTION94
1.3552-1.38130.33331330.30612545X-RAY DIFFRACTION94
1.3813-1.40950.31631370.27752597X-RAY DIFFRACTION95
1.4095-1.44020.30931360.24932584X-RAY DIFFRACTION95
1.4402-1.47370.23431360.22052577X-RAY DIFFRACTION95
1.4737-1.51050.28441370.21552603X-RAY DIFFRACTION95
1.5105-1.55140.2491370.21932597X-RAY DIFFRACTION96
1.5514-1.5970.22231370.18992618X-RAY DIFFRACTION96
1.597-1.64850.19851390.14072641X-RAY DIFFRACTION96
1.6485-1.70750.18451380.13672611X-RAY DIFFRACTION96
1.7075-1.77580.16931400.13222654X-RAY DIFFRACTION97
1.7758-1.85660.16171410.12922679X-RAY DIFFRACTION97
1.8566-1.95450.18261410.13312676X-RAY DIFFRACTION97
1.9545-2.0770.1531410.13222688X-RAY DIFFRACTION98
2.077-2.23730.14561430.12442710X-RAY DIFFRACTION98
2.2373-2.46240.19761430.13442733X-RAY DIFFRACTION98
2.4624-2.81860.16821440.1472768X-RAY DIFFRACTION99
2.8186-3.55060.15861480.14122800X-RAY DIFFRACTION99
3.5506-35.73220.22191510.1722862X-RAY DIFFRACTION96

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