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- PDB-4pwf: Crystal structure of V30M mutant human transthyretin complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4pwf
TitleCrystal structure of V30M mutant human transthyretin complexed with ferulic acid phenethyl ester
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Tranporter / thyroxine binding
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-PWF / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYokoyama, T. / Kosaka, Y. / Mizuguchi, M.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin
Authors: Yokoyama, T. / Kosaka, Y. / Mizuguchi, M.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2824
Polymers34,6852
Non-polymers5972
Water1,838102
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5648
Polymers69,3704
Non-polymers1,1934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6770 Å2
ΔGint-44 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.070, 84.989, 64.614
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-

PWF

21A-201-

PWF

31B-201-

PWF

41B-201-

PWF

51A-350-

HOH

61B-338-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M30 / References: UniProt: P02766
#2: Chemical ChemComp-PWF / 2-phenylethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate


Mass: 298.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.7 Å3/Da / Density % sol: 27.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-30% PEG400, 0.1M HEPES, 0.2M CaCl2, 4mM ferulic acid phenethyl ester, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30.3 Å / Num. all: 31016 / Num. obs: 30994 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.8 / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PWE

4pwe


Resolution: 1.6→30.25 Å / FOM work R set: 0.814 / SU ML: 0.25 / σ(F): 1.42 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1562 5.04 %RANDOM
Rwork0.2 ---
obs0.2017 30994 96.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.6 Å2 / Biso mean: 17.57 Å2 / Biso min: 1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 44 102 1918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071902
X-RAY DIFFRACTIONf_angle_d1.1012595
X-RAY DIFFRACTIONf_chiral_restr0.071288
X-RAY DIFFRACTIONf_plane_restr0.006330
X-RAY DIFFRACTIONf_dihedral_angle_d16.871685
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 (%)
1.6-1.65160.37491280.34662487261592
1.6516-1.71070.37121460.32432552269894
1.7107-1.77920.33341200.28932607272795
1.7792-1.86010.32111520.24372571272395
1.8601-1.95820.26181440.20672648279296
1.9582-2.08080.21331500.18892682283299
2.0808-2.24140.19911100.16862775288599
2.2414-2.46690.21361560.1782712286899
2.4669-2.82370.22641440.18842736288098
2.8237-3.55660.21211480.18272798294699
3.5566-30.2550.20851640.18632864302897

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