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- PDB-1soq: Crystal structure of the transthyretin mutant A108Y/L110E solved ... -

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Basic information

Entry
Database: PDB / ID: 1soq
TitleCrystal structure of the transthyretin mutant A108Y/L110E solved in space group C2
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / GREEK KEY BETA BARREL
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / : / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHornberg, A. / Olofsson, A. / Eneqvist, T. / Lundgren, E. / Sauer-Eriksson, A.E.
CitationJournal: Biochim.Biophys.Acta / Year: 2004
Title: The beta-strand D of transthyretin trapped in two discrete conformations
Authors: Hornberg, A. / Olofsson, A. / Eneqvist, T. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 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 1.5Aug 23, 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
C: Transthyretin
D: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers55,5424
Non-polymers00
Water2,828157
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers55,5424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6510 Å2
ΔGint-43 kcal/mol
Surface area19160 Å2
MethodPISA, PQS
2
C: Transthyretin
D: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,7712
Polymers27,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-43 kcal/mol
Surface area19520 Å2
MethodPISA
3
C: Transthyretin
D: Transthyretin

C: Transthyretin
D: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,5424
Polymers55,5424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)101.287, 67.524, 80.978
Angle α, β, γ (deg.)90.00, 112.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13885.413 Da / Num. of mol.: 4 / Mutation: A108Y, L110E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 291 K / pH: 6
Details: Tris, PEG550MME, ammonium sulfate, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 29735 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.7 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SOK

1sok


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.065 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.201
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1423 5.1 %RANDOM
Rwork0.21 ---
obs0.212 28177 --
all-29735 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 0 157 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213748
X-RAY DIFFRACTIONr_bond_other_d0.0010.023260
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9335141
X-RAY DIFFRACTIONr_angle_other_deg0.75537603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5443478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82415618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024226
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02774
X-RAY DIFFRACTIONr_nbd_refined0.2140.3593
X-RAY DIFFRACTIONr_nbd_other0.220.33004
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.5286
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.389
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.52338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36423822
X-RAY DIFFRACTIONr_scbond_it1.72131410
X-RAY DIFFRACTIONr_scangle_it2.8564.51319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 109
Rwork0.266 1898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8783-0.1904-0.76252.09250.46681.26450.0161-0.0438-0.11050.2367-0.0812-0.29630.1280.04370.06510.02850.0142-0.05630.17090.03850.138560.04561.99844.2499
21.0635-0.18210.2951.0871-0.51391.41420.0720.05070.32840.0547-0.11710.2318-0.13350.02870.04510.01660.03630.00580.186-0.01310.246440.671127.3233-1.3052
32.70640.7173-0.37590.4668-0.46471.264-0.089-0.10670.22780.03580.0677-0.0897-0.12560.05880.02120.0777-0.0312-0.040.1693-0.04750.122946.867829.388542.7744
41.8131-0.12931.03460.4296-0.47032.43770.24560.1176-0.44390.05630.0946-0.05270.08070.2108-0.34010.04280.0343-0.0910.1613-0.05840.212447.58369.436639.9027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 12510 - 125
2X-RAY DIFFRACTION2BB10 - 12410 - 124
3X-RAY DIFFRACTION3CC10 - 12510 - 125
4X-RAY DIFFRACTION4DD10 - 12410 - 124

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