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- PDB-5boj: Crystal Structure of Human Transthyretin in Complex with Gemfibrozil -

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Basic information

Entry
Database: PDB / ID: 5boj
TitleCrystal Structure of Human Transthyretin in Complex with Gemfibrozil
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Thyroxine binding / Gemfibrozil 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-4TX / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBegum, A. / Olofsson, A. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Med.Chem. / Year: 2015
Title: Enthalpic Forces Correlate with the Selectivity of Transthyretin-Stabilizing Ligands in Human Plasma.
Authors: Iakovleva, I. / Brannstrom, K. / Nilsson, L. / Gharibyan, A.L. / Begum, A. / Anan, I. / Walfridsson, M. / Sauer-Eriksson, A.E. / Olofsson, A.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)28,0785
Polymers27,5552
Non-polymers5243
Water4,396244
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,15710
Polymers55,1094
Non-polymers1,0476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.685, 85.409, 63.624
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-

4TX

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-4TX / 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid


Mass: 250.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22O3 / Comment: medication*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: TTRwt was dialyzed against 10 mM sodium phosphate with 100 mM KCl pH 7.6 and concentrated to 5 mg/ml. The resevoir contained 1.3-1.6 M sodium citrate and 3.5% glycerol at pH 5.5. Drop size 3 plus 3 microliter.
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. obs: 23805 / % possible obs: 98.6 % / Redundancy: 10 % / Rsym value: 0.063 / Net I/σ(I): 28.95
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.45 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SAINTdata reduction
SADABSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.75→21.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1187 5 %Random selection
Rwork0.17 ---
obs0.172 23722 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 37 244 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112057
X-RAY DIFFRACTIONf_angle_d1.4012844
X-RAY DIFFRACTIONf_dihedral_angle_d14.815777
X-RAY DIFFRACTIONf_chiral_restr0.054316
X-RAY DIFFRACTIONf_plane_restr0.008369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.82980.30511310.25732510X-RAY DIFFRACTION89
1.8298-1.92620.2831410.21892761X-RAY DIFFRACTION98
1.9262-2.04680.25891420.20032823X-RAY DIFFRACTION100
2.0468-2.20470.22711390.18622833X-RAY DIFFRACTION100
2.2047-2.42630.22161470.17432851X-RAY DIFFRACTION100
2.4263-2.77670.23341540.17232843X-RAY DIFFRACTION100
2.7767-3.49590.1911700.15232891X-RAY DIFFRACTION100
3.4959-21.35380.16811630.14013023X-RAY DIFFRACTION100

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