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- PDB-3djt: Crystal structure of transthyretin variant V30M at acidic pH -

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Basic information

Entry
Database: PDB / ID: 3djt
TitleCrystal structure of transthyretin variant V30M 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


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / 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: 2.3 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)27,6192
Polymers27,6192
Non-polymers00
Water2,450136
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,2384
Polymers55,2384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6320 Å2
ΔGint-45 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.782, 86.064, 64.231
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-154-

HOH

21B-128-

HOH

31B-159-

HOH

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Components

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


Mass: 13809.426 Da / Num. of mol.: 2 / Mutation: V30M
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 / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6
Details: 32% PEG 2000, 0.1M NaAc, 0.2M Am2SO4 , pH 4.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9859 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9859 Å / Relative weight: 1
ReflectionResolution: 2.2→86.07 Å / Num. all: 12491 / Num. obs: 12491 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1716 / % possible all: 94.9

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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: 2.3→51.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.506 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.449 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25338 526 4.8 %RANDOM
Rwork0.21313 ---
obs0.2151 10880 97.82 %-
all-12491 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.85 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 136 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9432581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86623.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44515293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.739159
X-RAY DIFFRACTIONr_chiral_restr0.1350.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21234
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.80221220
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.27731934
X-RAY DIFFRACTIONr_scbond_it5.42770
X-RAY DIFFRACTIONr_scangle_it7.1123647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 35 -
Rwork0.315 722 -
obs-722 98.7 %

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