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- PDB-8dw5: Complex of Human Transthyretin with 3',5'-Dichlorophenylanthranil... -

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Basic information

Entry
Database: PDB / ID: 8dw5
TitleComplex of Human Transthyretin with 3',5'-Dichlorophenylanthranilic Acid
ComponentsTransthyretin
KeywordsPROTEIN TRANSPORT / thyroid hormone distributor protein / amyloidogenic protein
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
2-[(3,5-dichlorophenyl)amino]benzoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsTruong, J.Q. / Holdsworth, B. / Holien, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2022
Title: Structural Analysis of the Complex of Human Transthyretin with 3',5'-Dichlorophenylanthranilic Acid at 1.5 angstrom Resolution.
Authors: Cody, V. / Truong, J.Q. / Holdsworth, B.A. / Holien, J.K. / Richardson, S.J. / Chalmers, D.K. / Craik, D.J.
History
DepositionJul 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7982
Polymers15,5161
Non-polymers2821
Water66737
1
A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1948
Polymers62,0654
Non-polymers1,1284
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)41.198, 64.079, 84.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

FQ7

21A-201-

FQ7

31A-303-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 15516.362 Da / Num. of mol.: 1
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-FQ7 / 2-[(3,5-dichlorophenyl)amino]benzoic acid


Mass: 282.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9Cl2NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.81 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.71 / Details: 1.3 M sodium citrate pH 5.71, 3% glycerol / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.52→51.06 Å / Num. obs: 17632 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Χ2: 0.94 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.33-51.0610.30.05529.81320.9980.0180.0581.1199.2
1.52-1.55133.93118590.3091.073.9310.88100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THA

1tha


Resolution: 1.52→42.26 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 1763 10 %
Rwork0.1971 15861 -
obs0.2008 17624 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.57 Å2
Refinement stepCycle: LAST / Resolution: 1.52→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 18 37 947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136949
X-RAY DIFFRACTIONf_angle_d1.65821301
X-RAY DIFFRACTIONf_chiral_restr0.1066146
X-RAY DIFFRACTIONf_plane_restr0.0144166
X-RAY DIFFRACTIONf_dihedral_angle_d17.2773329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.36771330.33741192X-RAY DIFFRACTION99.85
1.56-1.610.31211330.32751198X-RAY DIFFRACTION100
1.61-1.660.37771350.3281216X-RAY DIFFRACTION100
1.66-1.720.40151330.30881201X-RAY DIFFRACTION100
1.72-1.790.29741340.24751209X-RAY DIFFRACTION99.93
1.79-1.870.25421330.21311193X-RAY DIFFRACTION100
1.87-1.970.25221360.19751226X-RAY DIFFRACTION100
1.97-2.090.21391330.19571192X-RAY DIFFRACTION100
2.09-2.250.21321340.16551210X-RAY DIFFRACTION99.85
2.25-2.480.21891380.1881237X-RAY DIFFRACTION99.93
2.48-2.840.24161370.18861230X-RAY DIFFRACTION100
2.84-3.570.20721380.1791248X-RAY DIFFRACTION100
3.58-42.260.21971460.18231309X-RAY DIFFRACTION99.79

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