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- PDB-5l4m: Crystal Structure of Human Transthyretin in Complex with 3,5,6-Tr... -

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Basic information

Entry
Database: PDB / ID: 5l4m
TitleCrystal Structure of Human Transthyretin in Complex with 3,5,6-Trichloro-2-pyridinyloxyacetic acid (Triclopyr)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine binding / 3 / 5 / 6-Trichloro-2-pyridinyloxyacetic acid (Triclopyr) 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
Triclopyr / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsGrundstrom, C. / Hall, M. / Zhang, J. / Olofsson, A. / Andersson, P. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Environ. Sci. Technol. / Year: 2016
Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.
Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)28,0915
Polymers27,5552
Non-polymers5363
Water3,675204
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18110
Polymers55,1094
Non-polymers1,0726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7110 Å2
ΔGint-48 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.543, 85.520, 64.012
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-

SBK

21A-201-

SBK

31B-201-

SBK

41B-201-

SBK

51B-321-

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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-SBK / Triclopyr / Triclopyr


Mass: 256.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4Cl3NO3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Purified TTRwt was dialyzed against 10 mM sodium phosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. Triclopyr was added at 5 x molar excess to the protein. The ...Details: Purified TTRwt was dialyzed against 10 mM sodium phosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. Triclopyr was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter

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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: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→27.3 Å / Num. obs: 31035 / % possible obs: 94.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.4 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.581→27.282 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.09
RfactorNum. reflection% reflection
Rfree0.1982 2792 4.97 %
Rwork0.1596 --
obs0.1615 31035 90.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.581→27.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 29 204 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042019
X-RAY DIFFRACTIONf_angle_d0.6542778
X-RAY DIFFRACTIONf_dihedral_angle_d14.2791213
X-RAY DIFFRACTIONf_chiral_restr0.052306
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5815-1.60870.3986950.36711837X-RAY DIFFRACTION62
1.6087-1.6380.3261410.31572678X-RAY DIFFRACTION90
1.638-1.66950.28671380.2842556X-RAY DIFFRACTION89
1.6695-1.70350.34241420.28132655X-RAY DIFFRACTION90
1.7035-1.74060.31411390.26592630X-RAY DIFFRACTION90
1.7406-1.78110.29281420.24852641X-RAY DIFFRACTION90
1.7811-1.82560.23541390.22672663X-RAY DIFFRACTION91
1.8256-1.87490.26511390.20292693X-RAY DIFFRACTION91
1.8749-1.93010.24111360.17422642X-RAY DIFFRACTION91
1.9301-1.99240.20271380.16372660X-RAY DIFFRACTION91
1.9924-2.06360.22651390.15422672X-RAY DIFFRACTION92
2.0636-2.14620.20151420.14392686X-RAY DIFFRACTION91
2.1462-2.24380.19431410.13422718X-RAY DIFFRACTION93
2.2438-2.3620.17921410.13542727X-RAY DIFFRACTION93
2.362-2.50990.19681440.13342726X-RAY DIFFRACTION93
2.5099-2.70350.18961420.13562769X-RAY DIFFRACTION95
2.7035-2.97530.16691500.14122824X-RAY DIFFRACTION96
2.9753-3.40520.17441500.12822830X-RAY DIFFRACTION97
3.4052-4.28740.141500.11842881X-RAY DIFFRACTION98
4.2874-27.28650.16071440.1492862X-RAY DIFFRACTION98

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