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- PDB-4pm1: Human transthyretin (TTR) complexed with 16-alpha-bromo-estradiol -

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Basic information

Entry
Database: PDB / ID: 4pm1
TitleHuman transthyretin (TTR) complexed with 16-alpha-bromo-estradiol
ComponentsTransthyretin
KeywordsThyroid hormone-binding protein / Human transthyretin hydrophobic ligand solubilization
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-ESZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsStura, E.A. / Ciccone, L.
CitationJournal: N Biotechnol / Year: 2014
Title: Transthyretin complexes with curcumin and bromo-estradiol: evaluation of solubilizing multicomponent mixtures.
Authors: Ciccone, L. / Tepshi, L. / Nencetti, S. / Stura, E.A.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _citation.country / _entity_src_nat.pdbx_alt_source_flag ..._citation.country / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _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 / refine_hist
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)28,3816
Polymers27,5552
Non-polymers8274
Water6,017334
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,76312
Polymers55,1094
Non-polymers1,6538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)43.202, 86.134, 63.395
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-

ESZ

21A-201-

ESZ

31B-203-

ESZ

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21-147 / Source method: isolated from a natural source / Details: Lyophilized prealbumin from Human plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-ESZ / (14beta,16alpha,17alpha)-16-bromoestra-1,3,5(10)-triene-3,17-diol


Mass: 351.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23BrO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5. Precipitant:: 70% (30% PEG 4000, 0.2M imidazole malate, pH 6.0) 30% (18% monomethyl PEG 2000, 0.1 M sodium ...Details: Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5. Precipitant:: 70% (30% PEG 4000, 0.2M imidazole malate, pH 6.0) 30% (18% monomethyl PEG 2000, 0.1 M sodium cacodylate, pH 6.5). Cryoprotectant: 40% (25 % diethylene glycol + 12.5 % MPD + 37.5 % 2,3-butanediol + 12.5 % 1,4-dioxane) 50% (12.5% MPEG 5K, 25% MPEG 550) 0.1 M (mixed Na propionate, Na cacodylate, Bis-Tris-propane 50% at pH 4.0 and 50% pH 9.5)
PH range: 6.0 - 6.5 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2014
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: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.23→43.067 Å / Num. all: 69505 / Num. obs: 68116 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.32 % / Rmerge(I) obs: 0.118 / Rsym value: 0.111 / Net I/σ(I): 11.73
Reflection shellResolution: 1.23→1.27 Å / Redundancy: 9.58 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.88 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
REFMACrefinement
Cootmodel building
XDSdata scaling
XSCALEdata scaling
ADSCMXcubedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GS4

3gs4


Resolution: 1.23→43.067 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 3416 5.02 %Random
Rwork0.1767 ---
obs0.1784 68063 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→43.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 50 334 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072275
X-RAY DIFFRACTIONf_angle_d1.3043153
X-RAY DIFFRACTIONf_dihedral_angle_d16.062857
X-RAY DIFFRACTIONf_chiral_restr0.05342
X-RAY DIFFRACTIONf_plane_restr0.007421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.24760.31191430.27832588X-RAY DIFFRACTION96
1.2476-1.26620.25861360.25762646X-RAY DIFFRACTION97
1.2662-1.2860.27361430.24852607X-RAY DIFFRACTION97
1.286-1.30710.28891350.24982631X-RAY DIFFRACTION97
1.3071-1.32960.25821320.2472610X-RAY DIFFRACTION97
1.3296-1.35380.29281370.24912685X-RAY DIFFRACTION97
1.3538-1.37980.23651310.23682600X-RAY DIFFRACTION97
1.3798-1.4080.25431580.22962646X-RAY DIFFRACTION98
1.408-1.43860.2941520.22552665X-RAY DIFFRACTION98
1.4386-1.47210.23721450.21172649X-RAY DIFFRACTION98
1.4721-1.50890.24581340.2032659X-RAY DIFFRACTION97
1.5089-1.54970.23751180.19512691X-RAY DIFFRACTION98
1.5497-1.59530.19521460.18182693X-RAY DIFFRACTION98
1.5953-1.64680.20121390.17582675X-RAY DIFFRACTION98
1.6468-1.70570.20451410.1732688X-RAY DIFFRACTION98
1.7057-1.7740.21021290.16852706X-RAY DIFFRACTION99
1.774-1.85470.16261600.16692720X-RAY DIFFRACTION99
1.8547-1.95250.18241380.15832731X-RAY DIFFRACTION99
1.9525-2.07480.20521300.15352733X-RAY DIFFRACTION99
2.0748-2.2350.17021560.15162724X-RAY DIFFRACTION99
2.235-2.45990.17881590.15482751X-RAY DIFFRACTION99
2.4599-2.81580.21951530.16992784X-RAY DIFFRACTION100
2.8158-3.54730.18011420.15412837X-RAY DIFFRACTION100
3.5473-43.09330.22911590.16692928X-RAY DIFFRACTION99

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