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- PDB-5cly: X-ray structure of TTR mutant - S52P at 1.23A resolution -

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Basic information

Entry
Database: PDB / ID: 5cly
TitleX-ray structure of TTR mutant - S52P at 1.23A resolution
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / ATTR / prealbumin
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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: 1.23 Å
AuthorsYee, A.W. / Moulin, M. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Cooper, J.B. / Forsyth, V.T.
CitationJournal: To Be Published
Title: X-ray structure of TTR mutant - S52P at 1.23A resolution
Authors: Yee, A.W. / Moulin, M. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Cooper, J.B. / Forsyth, V.T.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1863
Polymers28,0932
Non-polymers921
Water3,153175
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3716
Polymers56,1874
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6780 Å2
ΔGint-47 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.017, 85.929, 63.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-305-

HOH

21B-306-

HOH

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Components

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


Mass: 14046.725 Da / Num. of mol.: 2 / Fragment: residues 21-147 / Mutation: S52P
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.5M di-sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.23→63.964 Å / Num. all: 67662 / Num. obs: 67662 / % possible obs: 97.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.049 / Rsym value: 0.042 / Net I/av σ(I): 5.08 / Net I/σ(I): 13.5 / Num. measured all: 255231
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.23-1.33.80.7251.13560893900.4170.7251.794.1
1.3-1.383.70.4491.73349991390.2640.4492.696.4
1.38-1.473.90.2852.83371486860.1630.2854.297.7
1.47-1.593.70.15552984580800.0920.1556.897.3
1.59-1.743.90.098.42920075620.0510.0911.198.2
1.74-1.943.80.05213.62625369060.030.05217.898.9
1.94-2.253.80.03518.62322861110.020.03526.698.8
2.25-2.753.80.03119.71997852900.0180.0313199.6
2.75-3.893.80.0316.31545441110.0170.0337.399.3
3.89-35.6963.50.0410.4845223870.0240.0438.699.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MxCuBEdata collection
XDSdata reduction
SCALA3.3.20data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVL

4pvl


Resolution: 1.23→35.7 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.656 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.042
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 3409 5 %RANDOM
Rwork0.157 ---
obs0.1585 64225 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.94 Å2 / Biso mean: 25.514 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.23→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 12 181 1987
Biso mean--23.24 36.54 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191937
X-RAY DIFFRACTIONr_bond_other_d0.0010.021771
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9472657
X-RAY DIFFRACTIONr_angle_other_deg3.53634118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4035248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17224.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70315296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.817158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212201
X-RAY DIFFRACTIONr_gen_planes_other0.020.02431
X-RAY DIFFRACTIONr_mcbond_it4.7631.987961
X-RAY DIFFRACTIONr_mcbond_other4.2343.25960
X-RAY DIFFRACTIONr_mcangle_it4.8712.9621209
X-RAY DIFFRACTIONr_rigid_bond_restr15.9831927
X-RAY DIFFRACTIONr_sphericity_bonded24.35651865
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 233 -
Rwork0.335 4412 -
all-4645 -
obs--91.55 %

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