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- PDB-5e4a: Human transthyretin (TTR) complexed with (2,7-Dichloro-fluoren-9-... -

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Basic information

Entry
Database: PDB / ID: 5e4a
TitleHuman transthyretin (TTR) complexed with (2,7-Dichloro-fluoren-9-ylideneaminooxy)-acetic acid.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Fluorenone based Fibrillogenesis inhibitor / Transthyretin
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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
Chem-5JW / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCiccone, L. / Nencetti, S. / Rossello, A. / Orlandini, E. / Stura, E.A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell'IstruzionePRIN 20109MXHMR_007 Italy
CitationJournal: J Enzyme Inhib Med Chem / Year: 2016
Title: Synthesis and structural analysis of halogen substituted fibril formation inhibitors of Human Transthyretin (TTR).
Authors: Ciccone, L. / Nencetti, S. / Rossello, A. / Stura, E.A. / Orlandini, E.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7993
Polymers29,4772
Non-polymers3221
Water4,810267
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5986
Polymers58,9544
Non-polymers6442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.210, 85.990, 63.820
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-

5JW

21B-239-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14738.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-5JW / {[(2,7-dichloro-9H-fluoren-9-ylidene)amino]oxy}acetic acid


Mass: 322.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9Cl2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.84 % / Description: Prismatic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: TTR at 5 mg/ml + 1.6 milli-M inhibitor. Precipitant: 18% PEG4K, 0.08M imidazole malate, pH 6.0 and 13.5% PEG10K, 0.06M ammonium acetate, pH 4.5 Cryoprotectant: 10% diethylene glycol ...Details: Protein: TTR at 5 mg/ml + 1.6 milli-M inhibitor. Precipitant: 18% PEG4K, 0.08M imidazole malate, pH 6.0 and 13.5% PEG10K, 0.06M ammonium acetate, pH 4.5 Cryoprotectant: 10% diethylene glycol + 5% MPD + 15% 2,3-butanediol + 5% 1,4-dioxane, 25% MPEG 5K, 0.1 M mixed (Na acetate, ADA, Bicine - 60% at pH 4/40% at pH 10) 1 milli-M inhibitor.
PH range: 5.5-6.7 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo-nozzle
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87006 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2014 / Details: mirrors
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87006 Å / Relative weight: 1
ReflectionResolution: 1.33→43.21 Å / Num. all: 55430 / Num. obs: 55377 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.12 % / Rmerge(I) obs: 0.076 / Rsym value: 0.072 / Net I/σ(I): 14.92
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 9.23 % / Rmerge(I) obs: 1.86 / Mean I/σ(I) obs: 1.22 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ8

4tq8


Resolution: 1.33→42.99 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.468 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19239 2769 5 %RANDOM
Rwork0.13944 ---
obs0.14202 52608 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.33→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 21 267 2081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192300
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4521.9643198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93223.883103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01215371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7841513
X-RAY DIFFRACTIONr_chiral_restr0.1880.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8671.8261133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6252.7261469
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2852.3251167
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.24418.7883692
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.78932300
X-RAY DIFFRACTIONr_sphericity_free45.611575
X-RAY DIFFRACTIONr_sphericity_bonded18.65852397
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 201 -
Rwork0.337 3831 -
obs--99.83 %

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