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- PDB-4deu: Crystal Structure of the Wild Type TTR Binding Naringenin (TTRwt:NAR) -

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Basic information

Entry
Database: PDB / ID: 4deu
TitleCrystal Structure of the Wild Type TTR Binding Naringenin (TTRwt:NAR)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / beta sandwich / amyloidosis
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
NARINGENIN / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)26,75415
Polymers25,5492
Non-polymers1,20513
Water3,927218
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50830
Polymers51,0974
Non-polymers2,41126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11360 Å2
ΔGint-16 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.734, 85.173, 65.058
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-205-

NAR

21A-205-

NAR

31A-205-

NAR

41A-205-

NAR

51B-202-

NAR

61B-202-

NAR

71B-202-

NAR

81B-202-

NAR

91B-399-

HOH

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Components

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


Mass: 12774.295 Da / Num. of mol.: 2 / Fragment: UNP residues 30-145
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAR / NARINGENIN / Naringenin


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
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: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2009
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.599→25 Å / Num. all: 29385 / Num. obs: 29385 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.064 / Χ2: 1.483 / Net I/σ(I): 11.1

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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 / Resolution: 1.599→22.254 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8645 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 1507 5.13 %
Rwork0.1893 --
obs0.1906 29385 89.48 %
all-29385 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.523 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 79.57 Å2 / Biso mean: 21.4597 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.3089 Å20 Å20 Å2
2--0.0131 Å20 Å2
3---5.2958 Å2
Refinement stepCycle: LAST / Resolution: 1.599→22.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 81 218 2089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0452141
X-RAY DIFFRACTIONf_angle_d2.0882934
X-RAY DIFFRACTIONf_chiral_restr0.17323
X-RAY DIFFRACTIONf_plane_restr0.013379
X-RAY DIFFRACTIONf_dihedral_angle_d15.036786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.599-1.6510.25631380.17142644278295
1.651-1.710.21921520.15952758291099
1.71-1.77840.22161430.14527872930100
1.7784-1.85940.19981600.154127782938100
1.8594-1.95730.2554980.20591836193465
1.9573-2.07990.18761370.160728192956100
2.0799-2.24030.19841250.16962193231878
2.2403-2.46550.21561310.20092224235579
2.4655-2.82170.20981490.17728583007100
2.8217-3.55270.19721480.17152546269498
3.5527-22.25580.18061260.18772435256185

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