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- PDB-3bt0: Crystal structure of transthyretin variant V20S -

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Basic information

Entry
Database: PDB / ID: 3bt0
TitleCrystal structure of transthyretin variant V20S
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / AMYLOID FIBRILS / POINT MUTATION
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsZanotti, G. / Folli, C. / Cendron, L. / Gliubich, F. / Negro, A. / Berni, R.
Citation
Journal: Febs J. / Year: 2008
Title: Structural and mutational analyses of protein-protein interactions between transthyretin and retinol-binding protein.
Authors: Zanotti, G. / Folli, C. / Cendron, L. / Alfieri, B. / Nishida, S.K. / Gliubich, F. / Pasquato, N. / Negro, A. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin.
Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: A comparative analysis of 23 structures of the amyloidogenic protein transthyretin.
Authors: Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,5312
Polymers27,5312
Non-polymers00
Water2,522140
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,0614
Polymers55,0614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6350 Å2
ΔGint-43 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.999, 83.812, 65.580
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 / Prealbumin / TBPA / TTR / ATTR


Mass: 13765.308 Da / Num. of mol.: 2 / Mutation: V20S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.066M CaCl2, 19% (w/v) PEG 400, 0.13M sodium Hepes , pH 7.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.59→65.51 Å / Num. all: 30276 / Num. obs: 30276 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.3
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2071 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.59→22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.701 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22911 1618 5.1 %RANDOM
Rwork0.20862 ---
all0.2102 32076 --
obs0.20966 30276 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.59→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 140 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221839
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9442511
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6615232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34923.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47215282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.53158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2729
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21233
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.96521188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52131879
X-RAY DIFFRACTIONr_scbond_it2.0122726
X-RAY DIFFRACTIONr_scangle_it2.9683630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.585→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 117 -
Rwork0.277 2071 -
obs--92.91 %

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