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- PDB-3w3b: Crystal structure of wild-type human transthyretin -

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Basic information

Entry
Database: PDB / ID: 3w3b
TitleCrystal structure of wild-type human transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloid / tranthyretin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLima, L.M.T.R.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of wild-type human transthyretin
Authors: Lima, L.M.T.R.
History
DepositionDec 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)27,5552
Polymers27,5552
Non-polymers00
Water2,684149
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,1094
Polymers55,1094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6080 Å2
ΔGint-46 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 83.490, 63.500
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
11A-221-

HOH

21B-211-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
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.: 149 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.9→63.5 Å / Num. all: 17774 / Num. obs: 17774 / % possible obs: 97 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 19.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-23.10.3020.2542.8773824600.1620.3020.2543.293.7
2-2.123.10.1960.1654.3724323270.1040.1960.1655.394
2.12-2.273.10.1480.1245.4688122140.080.1480.1248.195.4
2.27-2.453.10.1250.1056.5661121260.0670.1250.10510.296.8
2.45-2.693.20.0950.088.5635519910.0520.0950.0815.498.8
2.69-33.30.0740.06210.9607018480.040.0740.06223.699.7
3-3.473.30.0560.04712.9538516380.0310.0560.04735.899.7
3.47-4.253.20.0490.04113.8455314190.0270.0490.04148.999.9
4.25-6.013.20.0420.03514.9351511020.0230.0420.03554.599.8
6.01-21.84930.0340.02816.319366490.0190.0340.02848.697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å21.85 Å
Translation3.5 Å21.85 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTA

1tta


Resolution: 1.9→21.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2105 / WRfactor Rwork: 0.1644 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8385 / SU B: 4.081 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1885 / SU Rfree: 0.1686 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 909 5.1 %RANDOM
Rwork0.1796 ---
obs0.1823 17746 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.65 Å2 / Biso mean: 29.4994 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2---0.5 Å2-0 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 0 149 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192190
X-RAY DIFFRACTIONr_bond_other_d0.0020.021979
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9323034
X-RAY DIFFRACTIONr_angle_other_deg0.91934599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4323.592103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1371513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02526
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 71 -
Rwork0.256 1162 -
all-1233 -
obs--92.71 %

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