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- PDB-7y1i: Crystal Structure of TTR-G67R -

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Basic information

Entry
Database: PDB / ID: 7y1i
TitleCrystal Structure of TTR-G67R
ComponentsTransthyretin
KeywordsTRANSFERASE / Transthyretin
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: 2.79 Å
AuthorsLuan, X.D. / Chen, B.X. / Zhang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of TTR-G67R
Authors: Luan, X.D. / Chen, B.X. / Zhang, S.Y.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
I: Transthyretin
J: Transthyretin
K: Transthyretin
L: Transthyretin
M: Transthyretin
N: Transthyretin
O: Transthyretin
P: Transthyretin
Q: Transthyretin
R: Transthyretin
S: Transthyretin
T: Transthyretin
U: Transthyretin
V: Transthyretin
W: Transthyretin
X: Transthyretin


Theoretical massNumber of molelcules
Total (without water)382,48924
Polymers382,48924
Non-polymers00
Water00
1
A: Transthyretin
B: Transthyretin
E: Transthyretin
F: Transthyretin
I: Transthyretin
J: Transthyretin
K: Transthyretin
L: Transthyretin


Theoretical massNumber of molelcules
Total (without water)127,4968
Polymers127,4968
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transthyretin
D: Transthyretin
G: Transthyretin
H: Transthyretin

M: Transthyretin
N: Transthyretin
O: Transthyretin
P: Transthyretin


Theoretical massNumber of molelcules
Total (without water)127,4968
Polymers127,4968
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_564-x+y,-x+1,z-1/31
3
Q: Transthyretin
R: Transthyretin
S: Transthyretin
T: Transthyretin
U: Transthyretin
V: Transthyretin
W: Transthyretin
X: Transthyretin


Theoretical massNumber of molelcules
Total (without water)127,4968
Polymers127,4968
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.982, 140.982, 165.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

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


Mass: 15937.049 Da / Num. of mol.: 24
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

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: AMMONIUM SULFATE, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 101651 / % possible obs: 99.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 55.38 Å2 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 2.79→2.98 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4059 / Rpim(I) all: 0.516 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N85

4n85


Resolution: 2.79→46.15 Å / SU ML: 0.4589 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 38.423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3139 4607 5.04 %
Rwork0.2724 86730 -
obs0.2745 91337 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.94 Å2
Refinement stepCycle: LAST / Resolution: 2.79→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22028 0 0 0 22028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012322594
X-RAY DIFFRACTIONf_angle_d1.718630779
X-RAY DIFFRACTIONf_chiral_restr0.10813480
X-RAY DIFFRACTIONf_plane_restr0.00693918
X-RAY DIFFRACTIONf_dihedral_angle_d20.74237986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.820.361450.39312903X-RAY DIFFRACTION97.01
2.82-2.850.35881620.36192849X-RAY DIFFRACTION99.83
2.85-2.890.40021560.35422887X-RAY DIFFRACTION99.84
2.89-2.920.37271320.34172872X-RAY DIFFRACTION99.87
2.92-2.960.37541400.33082921X-RAY DIFFRACTION99.87
2.96-30.34631720.32662971X-RAY DIFFRACTION99.97
3-3.050.37321900.31882810X-RAY DIFFRACTION99.93
3.05-3.090.3512040.33022853X-RAY DIFFRACTION99.87
3.09-3.140.40021440.33392911X-RAY DIFFRACTION99.9
3.14-3.190.38541420.32162901X-RAY DIFFRACTION99.77
3.19-3.250.35881590.32312895X-RAY DIFFRACTION99.71
3.25-3.30.34041620.31632884X-RAY DIFFRACTION99.71
3.31-3.370.38141240.30072957X-RAY DIFFRACTION99.81
3.37-3.440.32691440.29342899X-RAY DIFFRACTION99.8
3.44-3.510.34821560.29512913X-RAY DIFFRACTION99.97
3.51-3.590.28231300.28212872X-RAY DIFFRACTION99.87
3.59-3.680.37111800.33222884X-RAY DIFFRACTION99.51
3.68-3.780.31731360.29412851X-RAY DIFFRACTION99.63
3.78-3.890.32541780.2842899X-RAY DIFFRACTION99.87
3.89-4.020.30191250.2792948X-RAY DIFFRACTION99.81
4.02-4.160.33491340.27032909X-RAY DIFFRACTION99.97
4.16-4.330.35561700.24132906X-RAY DIFFRACTION100
4.33-4.530.24731720.22392897X-RAY DIFFRACTION100
4.53-4.760.28581500.21952859X-RAY DIFFRACTION100
4.77-5.060.2981400.22612914X-RAY DIFFRACTION99.97
5.06-5.450.28751260.23712936X-RAY DIFFRACTION99.9
5.45-60.28851480.24522906X-RAY DIFFRACTION99.93
6-6.870.30741470.25822880X-RAY DIFFRACTION99.93
6.87-8.640.26691600.23912915X-RAY DIFFRACTION99.81
8.65-46.150.24181790.20832728X-RAY DIFFRACTION95.25

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