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- PDB-4y9f: Crystal structure of V30M mutated transthyretin with bromide in c... -

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Basic information

Entry
Database: PDB / ID: 4y9f
TitleCrystal structure of V30M mutated transthyretin with bromide in complex with gamma-mangostin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN/INHIBITOR / transthyretin / inhibitor / natural pruduct / transporter / amyloidosis / TRANSPORT PROTEIN-INHIBITOR complex
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
BROMIDE ION / Chem-MKT / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYokoyama, T. / Mizuguchi, M.
CitationJournal: Sci Rep / Year: 2015
Title: Discovery of gamma-Mangostin as an Amyloidogenesis Inhibitor
Authors: Yokoyama, T. / Ueda, M. / Ando, Y. / Mizuguchi, M.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,11712
Polymers34,6852
Non-polymers1,43210
Water3,171176
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,23524
Polymers69,3704
Non-polymers2,86420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.043, 85.638, 63.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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, PALB / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M30 / References: UniProt: P02766
#2: Chemical ChemComp-MKT / 1,3,6,7-tetrahydroxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one / Gamma-mangostin


Mass: 396.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24O6
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 20% PEG400, 0.092 M MES, 0.1 M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.91714 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91714 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38151 / % possible obs: 99.5 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 37.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PWE

4pwe


Resolution: 1.5→28.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.469 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1894 5 %RANDOM
Rwork0.19331 ---
obs0.19472 35871 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2---0.17 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.5→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 66 176 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.9732594
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5123.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.271157
X-RAY DIFFRACTIONr_chiral_restr0.1250.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211441
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 145 -
Rwork0.286 2531 -
obs--96.22 %

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