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- PDB-3kgs: V30M mutant human transthyretin (TTR) (apoV30M) pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3kgs
TitleV30M mutant human transthyretin (TTR) (apoV30M) pH 7.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / TRANSTHYRETIN / AMYLOID / Amyloidosis / Hormone / Neuropathy / Polymorphism / Secreted / Thyroid hormone / Transport
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: 1.8 Å
AuthorsTrivella, D.B. / Polikarpov, I.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: implications to tetramer stability and ligand-binding.
Authors: Trivella, D.B. / Bleicher, L. / Palmieri, L.C. / Wiggers, H.J. / Montanari, C.A. / Kelly, J.W. / Lima, L.M. / Foguel, D. / Polikarpov, I.
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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
Water3,729207
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 area6220 Å2
ΔGint-43 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.388, 85.463, 64.233
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-212-

HOH

21B-131-

HOH

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Components

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


Mass: 13809.426 Da / Num. of mol.: 2 / Fragment: UNP residues 20-147 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / 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.: 207 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 26041 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 7.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F41

1f41


Resolution: 1.8→22.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.83 / SU B: 2.989 / SU ML: 0.095 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1114 5 %RANDOM
Rwork0.2 ---
obs0.202 22267 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.12 Å2 / Biso mean: 20.451 Å2 / Biso min: 7.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 207 1987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222022
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9482787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.523.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52615332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8221511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021573
X-RAY DIFFRACTIONr_nbd_refined0.1980.2904
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2209
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.241
X-RAY DIFFRACTIONr_mcbond_it0.6351.51284
X-RAY DIFFRACTIONr_mcangle_it1.08322052
X-RAY DIFFRACTIONr_scbond_it1.3613851
X-RAY DIFFRACTIONr_scangle_it2.0524.5719
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 82 -
Rwork0.243 1432 -
all-1514 -
obs--91.92 %

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