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- PDB-6e70: Structure of Wild Type Human Transthyretin in Complex with Diflunisal -

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Basic information

Entry
Database: PDB / ID: 6.0E+70
TitleStructure of Wild Type Human Transthyretin in Complex with Diflunisal
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / diflunisal
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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, 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
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.992 Å
AuthorsChung, K. / Saelices, L. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG048120 United States
CitationJournal: To Be Published
Title: Structural Variants of Transthyretin
Authors: Saelices, L. / Chung, K. / Esswein, S. / Chou, J. / Liang, W. / Li, J.H. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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 / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)25,7936
Polymers25,2122
Non-polymers5814
Water59433
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58612
Polymers50,4244
Non-polymers1,1618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8790 Å2
ΔGint-79 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.090, 84.320, 65.050
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-

1FL

21B-201-

1FL

31B-201-

1FL

41B-201-

1FL

51B-201-

1FL

61B-201-

1FL

71B-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 33 or resid 35...
21(chain B and (resid 10 through 33 or resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSPHEPHE(chain A and (resid 10 through 33 or resid 35...AA10 - 331 - 24
12LYSLYSVALVAL(chain A and (resid 10 through 33 or resid 35...AA35 - 7126 - 62
13ILEILETYRTYR(chain A and (resid 10 through 33 or resid 35...AA73 - 11464 - 105
14TYRTYRASNASN(chain A and (resid 10 through 33 or resid 35...AA116 - 124107 - 115
21CYSCYSPHEPHE(chain B and (resid 10 through 33 or resid 35...BB10 - 331 - 24
22LYSLYSVALVAL(chain B and (resid 10 through 33 or resid 35...BB35 - 7126 - 62
23ILEILETYRTYR(chain B and (resid 10 through 33 or resid 35...BB73 - 11464 - 105
24TYRTYRASNASN(chain B and (resid 10 through 33 or resid 35...BB116 - 124107 - 115

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Components

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


Mass: 12606.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P02766
#2: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal / Diflunisal


Mass: 250.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O3 / Comment: antiinflammatory*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (W/V) PEG-1000, 0.1M Imidazole, 0.2M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→65.05 Å / Num. obs: 16279 / % possible obs: 99.1 % / Redundancy: 6.293 % / Biso Wilson estimate: 39.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.076 / Χ2: 0.994 / Net I/σ(I): 13.46 / Num. measured all: 102436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.045.7950.6882.496143119810600.9090.75488.5
2.04-2.16.3140.5633.37356116811650.9590.61499.7
2.1-2.166.0190.4594.066699111611130.970.50399.7
2.16-2.236.0050.3435.266582109710960.9690.37699.9
2.23-2.36.6560.2766.77062106110610.9880.3100
2.3-2.386.6520.2576.986891103810360.9920.27999.8
2.38-2.476.6520.1978.616719101010100.9940.214100
2.47-2.576.5630.1610.1161369379350.9940.17499.8
2.57-2.696.3270.12712.0959419409390.9930.13999.9
2.69-2.825.8040.10313.7551958978950.9970.11399.8
2.82-2.976.5720.08517.4655478458440.9950.09299.9
2.97-3.156.7210.07120.4153908038020.9940.07799.9
3.15-3.376.6680.06223.3850747617610.9980.068100
3.37-3.646.3970.05725.1145237087070.9980.06299.9
3.64-3.996.040.0526.0939566556550.9980.055100
3.99-4.465.9450.04827.5235736016010.9980.053100
4.46-5.146.5460.04930.1435025355350.9980.054100
5.14-6.36.280.05629.2429394694680.9970.06199.8
6.3-8.915.3530.0626.8319703683680.9970.067100
8.91-65.055.430.0627.6512382282280.9970.067100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.992→65.05 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1622 10 %
Rwork0.1855 14603 -
obs0.19 16225 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.26 Å2 / Biso mean: 50.1335 Å2 / Biso min: 27.6 Å2
Refinement stepCycle: final / Resolution: 1.992→65.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 38 33 1849
Biso mean--86.86 48.62 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061892
X-RAY DIFFRACTIONf_angle_d0.8732588
X-RAY DIFFRACTIONf_chiral_restr0.062288
X-RAY DIFFRACTIONf_plane_restr0.006330
X-RAY DIFFRACTIONf_dihedral_angle_d16.9261102
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1007X-RAY DIFFRACTION9.409TORSIONAL
12B1007X-RAY DIFFRACTION9.409TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9925-2.05110.341180.2791073119189
2.0511-2.11730.2761330.2251191132499
2.1173-2.1930.27281330.21221193132699
2.193-2.28080.25721350.198512111346100
2.2808-2.38460.30191340.20771208134299
2.3846-2.51030.24661350.20212171352100
2.5103-2.66760.28031360.194512201356100
2.6676-2.87360.24521340.210712221356100
2.8736-3.16280.26211350.204612211356100
3.1628-3.62040.20641390.178212501389100
3.6204-4.56110.16051400.151712601400100
4.5611-65.08470.24031500.180813371487100
Refinement TLS params.Method: refined / Origin x: 43.1178 Å / Origin y: 29.3929 Å / Origin z: 81.2155 Å
111213212223313233
T0.2933 Å2-0.0141 Å2-0.0071 Å2-0.2369 Å2-0.0251 Å2--0.3376 Å2
L1.2155 °2-0.1725 °2-0.5941 °2-1.0681 °2-0.2131 °2--1.6062 °2
S-0.0654 Å °0.1214 Å °-0.2899 Å °-0.0592 Å °0.0057 Å °0.0112 Å °0.1441 Å °-0.0504 Å °0.0277 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 124
2X-RAY DIFFRACTION1allB10 - 124
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 13
5X-RAY DIFFRACTION1allD14 - 33
6X-RAY DIFFRACTION1allE1 - 2

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