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- PDB-3p3s: Human transthyretin (TTR) complexed with (Z)-5-(3,5-dibromo-4-hyd... -

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Basic information

Entry
Database: PDB / ID: 3p3s
TitleHuman transthyretin (TTR) complexed with (Z)-5-(3,5-dibromo-4-hydroxybenzylidene)-imino-1-methylimidazolidin-4-one
ComponentsTransthyretin
Keywordshormone-binding protein / Hormone / T4 / Retinol Binding Protein
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
Chem-3M2 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: Sci Transl Med / Year: 2011
Title: Potent kinetic stabilizers that prevent transthyretin-mediated cardiomyocyte proteotoxicity.
Authors: Alhamadsheh, M.M. / Connelly, S. / Cho, A. / Reixach, N. / Powers, E.T. / Pan, D.W. / Wilson, I.A. / Kelly, J.W. / Graef, I.A.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Sep 6, 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)29,0556
Polymers27,5552
Non-polymers1,5004
Water1,51384
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,11012
Polymers55,1094
Non-polymers3,0008
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6320 Å2
ΔGint-43 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.110, 84.195, 64.888
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-128-

3M2

21A-128-

3M2

31A-128-

3M2

41A-128-

3M2

51B-128-

3M2

61B-128-

3M2

71B-128-

3M2

81B-128-

3M2

DetailsAsu contains 2 monomers of the tetramer. 2-fold axis splits the two symmetry related dimers.

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicuran Gold / References: UniProt: P02766
#2: Chemical
ChemComp-3M2 / (5Z)-2-amino-5-(3,5-dibromo-4-hydroxybenzylidene)-1-methyl-1,5-dihydro-4H-imidazol-4-one


Mass: 375.016 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H9Br2N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 43.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1. ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2010
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 32597 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.046 / Net I/σ(I): 32.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 6478 / Rsym value: 0.642 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FBR

2fbr


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2431 / WRfactor Rwork: 0.2107 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.7212 / SU B: 3.936 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1379 / SU Rfree: 0.0983 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1654 5.1 %RANDOM
Rwork0.2042 ---
obs0.2057 32564 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.42 Å2 / Biso mean: 25.963 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 72 84 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222080
X-RAY DIFFRACTIONr_bond_other_d0.0010.021366
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9922880
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0023352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6635280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64924.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65915334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2931510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212368
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02414
X-RAY DIFFRACTIONr_mcbond_it1.7171.51235
X-RAY DIFFRACTIONr_mcbond_other0.8231.5494
X-RAY DIFFRACTIONr_mcangle_it2.75122035
X-RAY DIFFRACTIONr_scbond_it3.623845
X-RAY DIFFRACTIONr_scangle_it5.3744.5820
X-RAY DIFFRACTIONr_rigid_bond_restr1.92333446
X-RAY DIFFRACTIONr_sphericity_free9.361384
X-RAY DIFFRACTIONr_sphericity_bonded4.64933368
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 114 -
Rwork0.296 2215 -
all-2329 -
obs--97.08 %

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