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

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Basic information

Entry
Database: PDB / ID: 4pwj
TitleCrystal structure of V30M mutant human transthyretin complexed with nordihydroguaiaretic 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-30Z / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)35,2904
Polymers34,6852
Non-polymers6052
Water2,792155
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5808
Polymers69,3704
Non-polymers1,2094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6260 Å2
ΔGint-46 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.565, 85.391, 64.221
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-

30Z

21A-201-

30Z

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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-30Z / 4-[(2R,3S)-3-[(3,4-DIHYDROXYPHENYL)METHYL]-2-METHYLBUTYL]BENZENE-1,2-DIOL


Mass: 302.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.72 Å3/Da / Density % sol: 28.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-30% PEG400, 0.1M HEPES, 0.2M CaCl2, 8mM nordihydroguaiaretic 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-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: 1.55→33.21 Å / Num. all: 34065 / Num. obs: 32332 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 91.7

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Processing

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

4pwe


Resolution: 1.55→33.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.899 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21944 1726 5.1 %RANDOM
Rwork0.19843 ---
obs0.19957 32332 95.87 %-
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: 25.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20 Å2
2---0.83 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 44 155 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9662622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58423.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.26158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211461
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: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 127 -
Rwork0.326 2200 -
obs--90.79 %

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