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- PDB-9rto: Room temperature crystal structure of the perdeuterated TTR mutan... -

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Basic information

Entry
Database: PDB / ID: 9rto
TitleRoom temperature crystal structure of the perdeuterated TTR mutant V30M at pH5.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin Amyloidosis V30M mutation Familial amyloidotic polyneuropath
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / 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 / protein-containing complex binding / protein-containing complex / 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: 1.56 Å
AuthorsSagot, J. / Fisher, S.Z. / Forsyth, T.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Room temperature crystal structure of the perdeuterated TTR mutant V30M at pH5.
Authors: Sagot, J. / Fisher, S.Z. / Forsyth, T.V.
History
DepositionJul 3, 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
Water1,45981
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
point symmetry operation2_655-x+1,y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)43.703, 65.134, 85.189
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-226-

HOH

21B-226-

HOH

31B-239-

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.: 81 / 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: 2.41 Å3/Da / Density % sol: 48.9 % / Description: cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.7 M sodium malonate pH5

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Data collection

DiffractionMean temperature: 293 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: May 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.56→43.7 Å / Num. obs: 35449 / % possible obs: 99.92 % / Redundancy: 13.34 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 23
Reflection shellResolution: 1.56→1.61 Å / Redundancy: 12.97 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3457 / CC1/2: 0.928 / Rpim(I) all: 0.19 / Rrim(I) all: 0.689 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→21.17 Å / SU ML: 0.1485 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 1999 5.65 %
Rwork0.1756 33383 -
obs0.1769 35382 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.68 Å2
Refinement stepCycle: LAST / Resolution: 1.56→21.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 81 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051959
X-RAY DIFFRACTIONf_angle_d1.08582694
X-RAY DIFFRACTIONf_chiral_restr0.0788303
X-RAY DIFFRACTIONf_plane_restr0.0101346
X-RAY DIFFRACTIONf_dihedral_angle_d13.8625716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.25531390.22392319X-RAY DIFFRACTION99.27
1.6-1.640.27051400.20442345X-RAY DIFFRACTION100
1.64-1.690.20981410.20352345X-RAY DIFFRACTION100
1.69-1.740.26061410.19092369X-RAY DIFFRACTION100
1.74-1.810.24291410.19272362X-RAY DIFFRACTION100
1.81-1.880.21191420.18182360X-RAY DIFFRACTION100
1.88-1.960.19471420.1692362X-RAY DIFFRACTION100
1.96-2.070.19511410.16552373X-RAY DIFFRACTION100
2.07-2.20.16061420.1642368X-RAY DIFFRACTION100
2.2-2.370.18091430.16682381X-RAY DIFFRACTION100
2.37-2.60.18521440.18712410X-RAY DIFFRACTION100
2.6-2.980.23171440.18892407X-RAY DIFFRACTION100
2.98-3.750.20071460.1712432X-RAY DIFFRACTION99.96

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