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- PDB-9rsp: Cryogenic crystal structure of the perdeuterated TTR mutant V30M ... -

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Basic information

Entry
Database: PDB / ID: 9rsp
TitleCryogenic crystal structure of the perdeuterated TTR mutant V30M at pH5.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin Amyloidosis V30M mutation Familial amyloidotic polyneuropathy
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid 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, 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSagot, J. / Fisher, S.Z. / Forsyth, T.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryogenic crystal structure of the perdeuterated TTR mutant V30M at pH5.
Authors: Sagot, J. / Fisher, S.Z. / Forsyth, T.V.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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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)25,2762
Polymers25,2762
Non-polymers00
Water3,135174
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)50,5534
Polymers50,5534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6280 Å2
ΔGint-45 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.276, 64.258, 85.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

21A-270-

HOH

31B-237-

HOH

41B-304-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12638.168 Da / Num. of mol.: 2 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.8 % / Description: cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.7 M Sodium Malonate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.61→43.29 Å / Num. obs: 31442 / % possible obs: 99.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.051 / Net I/σ(I): 33.7
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.359 / Num. unique obs: 3047 / CC1/2: 0.971 / Rrim(I) all: 0.374 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→21.33 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2006 1523 4.85 %
Rwork0.1722 29872 -
obs0.1736 31395 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.61→21.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 174 1952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561978
X-RAY DIFFRACTIONf_angle_d0.82552724
X-RAY DIFFRACTIONf_chiral_restr0.0579301
X-RAY DIFFRACTIONf_plane_restr0.0083359
X-RAY DIFFRACTIONf_dihedral_angle_d13.9459725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.26511450.20762632X-RAY DIFFRACTION98.76
1.66-1.720.20541290.19082694X-RAY DIFFRACTION99.47
1.72-1.790.231440.18492639X-RAY DIFFRACTION99.57
1.79-1.870.22311390.17892674X-RAY DIFFRACTION99.75
1.87-1.970.1721410.16812688X-RAY DIFFRACTION99.79
1.97-2.10.20431350.16792707X-RAY DIFFRACTION99.79
2.1-2.260.19781150.16462726X-RAY DIFFRACTION99.86
2.26-2.490.21041500.1822705X-RAY DIFFRACTION100
2.49-2.840.23421410.1812741X-RAY DIFFRACTION100
2.84-3.580.18681490.17012779X-RAY DIFFRACTION100

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