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- PDB-7tha: Crystal structure of human transthyretin variant C10A/M13V -

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Basic information

Entry
Database: PDB / ID: 7tha
TitleCrystal structure of human transthyretin variant C10A/M13V
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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, 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJaeger, M. / Mortenson, D.E. / Yan, N.L. / Kelly, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK046335 United States
CitationJournal: To Be Published
Title: Lysine carbamylation competes with urea unfolding of human transthyretin introducing kinetic heterogeneity
Authors: Jaeger, M. / Mortenson, D.E. / Yan, N.L. / Ardejani, M.S. / Kelly, J.W.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5475
Polymers27,4262
Non-polymers1203
Water2,774154
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,09310
Polymers54,8534
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area6770 Å2
ΔGint-94 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.602, 64.509, 85.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21B-341-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13713.230 Da / Num. of mol.: 2 / Mutation: C10A, M13V
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Crystals of TTR C10A/M13V were grown at 23 degrees C using sitting-drop vapor diffusion by mixing 0.2 microliters of 5 mg/mL protein in 50 mM Tris pH 7.8 and 0.2 microliters of a ...Details: Crystals of TTR C10A/M13V were grown at 23 degrees C using sitting-drop vapor diffusion by mixing 0.2 microliters of 5 mg/mL protein in 50 mM Tris pH 7.8 and 0.2 microliters of a crystallization buffer consisting of 0.19M CaCl2, 5% (v/v) glycerol, 0.095M HEPES pH 7.5, and 26.6% (v/v) PEG 400. Crystals were frozen directly without additional cryo-protection by plunging in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→42.96 Å / Num. obs: 24607 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 1 / Rpim(I) all: 0.026 / Rsym value: 0.067 / Net I/σ(I): 17.3
Reflection shellResolution: 1.75→1.84 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3541 / CC1/2: 0.73 / Rpim(I) all: 0.59 / Rsym value: 1.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDM

4ydm


Resolution: 1.75→32.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1275 5.2 %RANDOM
Rwork0.1813 ---
obs0.1829 23283 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.05 Å2 / Biso mean: 28.165 Å2 / Biso min: 17.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.75→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 3 154 1938
Biso mean--72.59 38.01 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131865
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171697
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6462560
X-RAY DIFFRACTIONr_angle_other_deg2.3681.5693945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92422.64487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76315282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.724158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022101
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02391
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 99 -
Rwork0.305 1682 -
all-1781 -
obs--99.89 %

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