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- PDB-3m1o: Human Transthyretin (TTR) complexed with 2-((3,5-dichloro-4-hydro... -

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Basic information

Entry
Database: PDB / ID: 3m1o
TitleHuman Transthyretin (TTR) complexed with 2-((3,5-dichloro-4-hydroxyphenyl)amino)benzoic acid
ComponentsTransthyretin
KeywordsHORMONE / AMYLOID / INHIBITOR / AMYLOIDOSIS / DISEASE MUTATION / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / NEUROPATHY / SECRETED / THYROID HORMONE / TRANSPORT
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/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-CJZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKolstoe, S.E. / Wood, S.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Trapping of palindromic ligands within native transthyretin prevents amyloid formation.
Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / ...Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / Smith, M.D. / Ley, S.V. / Robinson, C.V. / Wood, S.P. / Pepys, M.B.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)28,1514
Polymers27,5552
Non-polymers5962
Water4,486249
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3028
Polymers55,1094
Non-polymers1,1924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.525, 85.390, 63.625
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-

CJZ

21A-128-

CJZ

31A-128-

CJZ

41A-128-

CJZ

51A-128-

CJZ

61A-128-

CJZ

71B-128-

CJZ

81B-128-

CJZ

91B-128-

CJZ

101B-128-

CJZ

111B-128-

CJZ

121B-128-

CJZ

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


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-CJZ / 2-[(3,5-dichloro-4-hydroxyphenyl)amino]benzoic acid


Mass: 298.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Cl2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25- 32% V/V PEG550-MONOMETHYL ETHER, 70 MM NAAC BUFFER PH 4-5 AND 100 MM NACL, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→38.07 Å / Num. all: 73223 / Num. obs: 73223 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10525 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC& Phenix.refinerefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ROX

2rox


Resolution: 1.2→35.453 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3687 -RANDOM
Rwork0.143 ---
all0.144 73132 --
obs-73078 99.92 %-
Displacement parametersBiso mean: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.4915 Å2-0 Å20 Å2
2---0.887 Å2-0 Å2
3---0.3955 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 38 249 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfOND0.021
X-RAY DIFFRACTIONfNGLE1.851
X-RAY DIFFRACTIONfHIRALITY0.108
X-RAY DIFFRACTIONfLANARITY0.012
X-RAY DIFFRACTIONfIHEDRAL17.802
LS refinement shellResolution: 1.2→1.2158 Å
RfactorNum. reflection% reflection
Rfree0.222 124 -
Rwork0.1923 --
obs-2667 100 %

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