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- PDB-4ydn: High resolution crystal structure of human transthyretin bound to... -

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Basic information

Entry
Database: PDB / ID: 4ydn
TitleHigh resolution crystal structure of human transthyretin bound to ligand and conjugates of 4-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)phenyl fluorosulfate
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone transport protein / Thyroxine / retinol
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-2WN / Chem-4B8 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsConnelly, S. / Bradbury, N.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A Fluorogenic Aryl Fluorosulfate for Intraorganellar Transthyretin Imaging in Living Cells and in Caenorhabditis elegans.
Authors: Baranczak, A. / Liu, Y. / Connelly, S. / Du, W.G. / Greiner, E.R. / Genereux, J.C. / Wiseman, R.L. / Eisele, Y.S. / Bradbury, N.C. / Dong, J. / Noodleman, L. / Sharpless, K.B. / Wilson, I.A. ...Authors: Baranczak, A. / Liu, Y. / Connelly, S. / Du, W.G. / Greiner, E.R. / Genereux, J.C. / Wiseman, R.L. / Eisele, Y.S. / Bradbury, N.C. / Dong, J. / Noodleman, L. / Sharpless, K.B. / Wilson, I.A. / Encalada, S.E. / Kelly, J.W.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence ...entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,8465
Polymers27,7132
Non-polymers1,1343
Water2,810156
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,69310
Polymers55,4264
Non-polymers2,2676
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6190 Å2
ΔGint16.5 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.093, 85.522, 64.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

2WN

21A-201-

2WN

31A-201-

2WN

41A-201-

2WN

51A-202-

4B8

61A-202-

4B8

71A-202-

4B8

81B-201-

2WN

91B-201-

2WN

101B-201-

2WN

111B-201-

2WN

121B-201-

2WN

DetailsTetramer confirmed by by size exclusion chromatography

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13856.417 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 / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-2WN / 4-[5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenyl sulfurofluoridate


Mass: 405.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7Cl2FN2O5S
#3: Chemical ChemComp-4B8 / 2,6-dichloro-4-[5-(4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl]phenol


Mass: 323.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8Cl2N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.33 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals ...Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at ph 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 m sodium citrate, ph 5.5, containing 10% v/v glycerol, vapor diffusion, sitting drop, temperature 298.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationMonochromator: ASYMMETRIC CUT 4.965 DEGS SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.349→38.484 Å / Num. all: 53165 / Num. obs: 53165 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.6 Å2 / Rpim(I) all: 0.012 / Rrim(I) all: 0.031 / Rsym value: 0.028 / Net I/av σ(I): 13.804 / Net I/σ(I): 28.4 / Num. measured all: 338134
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.35-1.426.20.4491.64678375140.1940.4494.898
1.42-1.516.30.2762.64588572590.1190.2767.399.8
1.51-1.616.60.1554.64527568750.0650.15511.999.9
1.61-1.746.20.0997.23981263980.0430.09916.999.8
1.74-1.916.70.05612.73946359050.0230.05626.9100
1.91-2.136.30.03618.93393053610.0160.03640.499.8
2.13-2.466.60.02923.43122847600.0120.02951.499.8
2.46-3.026.20.02426.42506740430.0110.02459.199.8
3.02-4.276.20.01932.51990431970.0080.01974.399.4
4.27-38.4845.80.01731.61078718530.0080.01773.799.5

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.35→38.484 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1917 / WRfactor Rwork: 0.1581 / FOM work R set: 0.8886 / SU B: 1.625 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0572 / SU Rfree: 0.0556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 2693 5 %RANDOM
Rwork0.1574 50399 --
obs0.1591 50399 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.06 Å2 / Biso mean: 21.614 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.35→38.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 96 156 2041
Biso mean--23.09 33.46 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022082
X-RAY DIFFRACTIONr_bond_other_d0.0020.021866
X-RAY DIFFRACTIONr_angle_refined_deg1.6942.0132877
X-RAY DIFFRACTIONr_angle_other_deg1.3613.0034335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79123.64785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4811511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212364
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02471
X-RAY DIFFRACTIONr_mcbond_it2.0921.805974
X-RAY DIFFRACTIONr_mcbond_other2.0131.801973
X-RAY DIFFRACTIONr_mcangle_it2.4172.7081229
X-RAY DIFFRACTIONr_rigid_bond_restr3.01233948
X-RAY DIFFRACTIONr_sphericity_free20.602555
X-RAY DIFFRACTIONr_sphericity_bonded8.12853974
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 180 -
Rwork0.213 3531 -
all-3711 -
obs--95.99 %

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