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- PDB-4dew: Crystal Structure of the Wild Type TTR Binding Luteolin (TTRwt:LUT) -

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Basic information

Entry
Database: PDB / ID: 4dew
TitleCrystal Structure of the Wild Type TTR Binding Luteolin (TTRwt:LUT)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / beta sandwich / amyloidosis
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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/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-LU2 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsTrivella, D.B.B. / Polikarpov, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis.
Authors: Trivella, D.B. / Dos Reis, C.V. / Lima, L.M. / Foguel, D. / Polikarpov, I.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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.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 / _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)32,3824
Polymers31,8102
Non-polymers5722
Water2,306128
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7658
Polymers63,6204
Non-polymers1,1454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.264, 84.782, 65.087
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-201-

LU2

21A-201-

LU2

31A-201-

LU2

41A-201-

LU2

51A-201-

LU2

61A-201-

LU2

71B-201-

LU2

81B-201-

LU2

91B-201-

LU2

101B-201-

LU2

111B-201-

LU2

121B-201-

LU2

131A-330-

HOH

141B-316-

HOH

151B-324-

HOH

161B-343-

HOH

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

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
11CYSCYSASNASNchain A and (resseq 10:98 or resseq 104:123 )AA10 - 9830 - 118
12ARGARGTHRTHRchain A and (resseq 10:98 or resseq 104:123 )AA104 - 123124 - 143
21CYSCYSASNASNchain B and (resseq 10:98 or resseq 104:123 )BB10 - 9830 - 118
22ARGARGTHRTHRchain B and (resseq 10:98 or resseq 104:123 )BB104 - 123124 - 143

NCS oper: (Code: given
Matrix: (-0.993056, 0.117216, 0.010051), (0.117232, 0.993104, 0.000933), (-0.009872, 0.002105, -0.999949)
Vector: 37.619999, -2.41735, 97.711197)

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 15904.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.88 Å3/Da / Density % sol: 34.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2009
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.899→30 Å / Num. all: 19276 / Num. obs: 19276 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.077 / Χ2: 0.944 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.899-1.973.50.3817370.683190.2
1.97-2.053.80.30818540.728197.1
2.05-2.143.90.24318860.842198.8
2.14-2.2540.1919310.921199.8
2.25-2.3940.17319170.89199.6
2.39-2.5840.15519451.095199.9
2.58-2.844.10.1319431.1011100
2.84-3.2540.08219671.0311100
3.25-4.0940.05119880.9981100
4.09-303.80.0421081.042199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CFM

3cfm


Resolution: 1.899→26.007 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 987 5.13 %
Rwork0.1835 --
obs0.1843 19231 98.44 %
all-19231 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 88.8 Å2 / Biso mean: 28.0992 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.899→26.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 42 128 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0361890
X-RAY DIFFRACTIONf_angle_d1.6242591
X-RAY DIFFRACTIONf_chiral_restr0.178290
X-RAY DIFFRACTIONf_plane_restr0.011327
X-RAY DIFFRACTIONf_dihedral_angle_d17.754646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A838X-RAY DIFFRACTIONPOSITIONAL0.901
12B838X-RAY DIFFRACTIONPOSITIONAL0.901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.899-1.99960.23961150.21442386250192
1.9996-2.12480.20451200.19022580270098
2.1248-2.28880.20121590.177925842743100
2.2888-2.51890.2081600.193325962756100
2.5189-2.8830.22711440.18626532797100
2.883-3.63070.18751490.174126492798100
3.6307-26.00960.18111400.17822796293699

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