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- PDB-2b9a: Human transthyretin (TTR) complexed with diflunisal analogues- TT... -

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Basic information

Entry
Database: PDB / ID: 2b9a
TitleHuman transthyretin (TTR) complexed with diflunisal analogues- TTR.3',5'-difluorobiphenyl-4-carboxylic acid
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / TTR / AMYLOID / TRANSTHYRETIN / HORMONE-GROWTH FACTOR 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
3',5'-DIFLUOROBIPHENYL-4-CARBOXYLIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsPalaninathan, S.K. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Diflunisal Analogues Stabilize the Native State of Transthyretin. Potent Inhibition of Amyloidogenesis.
Authors: Adamski-Werner, S.L. / Palaninathan, S.K. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0234
Polymers27,5552
Non-polymers4682
Water3,441191
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0468
Polymers55,1094
Non-polymers9374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)42.935, 84.852, 63.742
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-301-

FBC

21A-301-

FBC

31A-301-

FBC

41A-301-

FBC

51B-302-

FBC

61B-302-

FBC

71B-302-

FBC

81B-302-

FBC

91B-302-

FBC

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 10 - 123 / Label seq-ID: 10 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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) / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-FBC / 3',5'-DIFLUOROBIPHENYL-4-CARBOXYLIC ACID


Mass: 234.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, 100 mM KCL, 1 mM EDTA, 10 mM sodium phosphate, soaked with the inhibitor, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.541 / Wavelength: 1 Å
DetectorType: CCD-PXL-L600 / Detector: CCD / Date: Jun 1, 2002
RadiationMonochromator: bent conical si mirror/Bent Ge monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.5411
211
ReflectionResolution: 1.54→42.18 Å / Num. all: 33741 / Num. obs: 33741 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.03
Reflection shellResolution: 1.54→1.6 Å / % possible all: 98

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMZ

1bmz


Resolution: 1.54→42.18 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 2.323 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24593 1693 5 %RANDOM
Rwork0.22234 ---
obs0.23099 33720 95.7 %-
all-33741 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.54→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 34 191 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0670.0221810
X-RAY DIFFRACTIONr_angle_refined_deg2.7241.9612470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20223.61172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021371
X-RAY DIFFRACTIONr_nbd_refined0.2380.2777
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.213
X-RAY DIFFRACTIONr_mcbond_it1.2651.51166
X-RAY DIFFRACTIONr_mcangle_it2.01421812
X-RAY DIFFRACTIONr_scbond_it2.8293833
X-RAY DIFFRACTIONr_scangle_it4.1134.5658
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 827 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.460.5
medium thermal1.822
LS refinement shellResolution: 1.54→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 100 -
Rwork0.242 3393 -
obs--98 %

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