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- PDB-3dk0: Crystal structure of transthyretin variant L55P at acidic pH -

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Basic information

Entry
Database: PDB / ID: 3dk0
TitleCrystal structure of transthyretin variant L55P at acidic pH
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / AMYLOID FIBRILS / POINT MUTATION / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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: 1.87 Å
AuthorsCendron, L. / Zanotti, G. / Folli, C. / Berni, R.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.
Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / 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
DepositionJun 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 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 1.4Nov 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)27,5232
Polymers27,5232
Non-polymers00
Water2,396133
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,0454
Polymers55,0454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6330 Å2
ΔGint-48 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.632, 84.780, 65.415
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-180-

HOH

21A-186-

HOH

31B-155-

HOH

41B-161-

HOH

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13761.317 Da / Num. of mol.: 2 / Mutation: L55P
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.: 133 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6
Details: 32% PEG 400, 0.05-0.2M CaCl2, 0.1M NaHepes , pH 4.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.85→51.3 Å / Num. all: 19735 / Num. obs: 19735 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2554 / % possible all: 89.7

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Processing

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

1f41


Resolution: 1.87→42.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.171 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1001 5.1 %RANDOM
Rwork0.20692 ---
obs0.20768 19703 96.78 %-
all-19703 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.87→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 133 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9452624
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25223.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47515290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.831510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021484
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.2635
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21249
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.16521205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.90731972
X-RAY DIFFRACTIONr_scbond_it5.5972707
X-RAY DIFFRACTIONr_scangle_it8.4973651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.867→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 62 -
Rwork0.326 1002 -
obs-1002 72.09 %

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