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

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Basic information

Entry
Database: PDB / ID: 4pwi
TitleCrystal structure of V30M mutant human transthyretin complexed with rosmarinic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transporter / 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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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-ROA / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 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 / 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)35,4064
Polymers34,6852
Non-polymers7212
Water2,432135
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8128
Polymers69,3704
Non-polymers1,4414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6120 Å2
ΔGint-46 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.150, 85.726, 63.774
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-

ROA

21B-201-

ROA

31B-201-

ROA

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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-ROA / (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid / Rosmarinic acid


Mass: 360.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 27.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-30% PEG400, 0.1M HEPES, 0.2M CaCl2, 9mM rosmarinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 17, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.494→27.449 Å / Num. all: 36487 / Num. obs: 36479 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.1 / % possible all: 89.1

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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: 1.494→27.449 Å / FOM work R set: 0.844 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1824 5 %RANDOM
Rwork0.1983 ---
obs0.2 36479 93.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.11 Å2 / Biso mean: 37.95 Å2 / Biso min: 25.83 Å2
Refinement stepCycle: LAST / Resolution: 1.494→27.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 52 135 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071872
X-RAY DIFFRACTIONf_angle_d1.1952555
X-RAY DIFFRACTIONf_chiral_restr0.071286
X-RAY DIFFRACTIONf_plane_restr0.006322
X-RAY DIFFRACTIONf_dihedral_angle_d13.734675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.494-1.53440.31311280.31652357248584
1.5344-1.57960.32441330.2862520265390
1.5796-1.63060.23961210.25352571269291
1.6306-1.68880.30551350.24612588272392
1.6888-1.75640.27621410.22222577271891
1.7564-1.83640.27491290.20232599272892
1.8364-1.93310.22061360.17872607274392
1.9331-2.05420.19351370.17272758289596
2.0542-2.21280.24581460.16732774292098
2.2128-2.43530.19841540.17472763291797
2.4353-2.78740.23111540.19842733288795
2.7874-3.51070.2081730.19572837301098
3.5107-27.45340.22651370.19132971310896

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