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- PDB-1f41: CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN AT 1.5A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1f41
TitleCRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN AT 1.5A RESOLUTION
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / Greek key beta barrel
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 / phototransduction, visible light / Non-integrin membrane-ECM interactions / 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 / phototransduction, visible light / Non-integrin membrane-ECM interactions / 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/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 / Resolution: 1.3 Å
AuthorsHornberg, A. / Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: A comparative analysis of 23 structures of the amyloidogenic protein transthyretin.
Authors: Hornberg, A. / Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,5552
Polymers27,5552
Non-polymers00
Water3,351186
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,1094
Polymers55,1094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6290 Å2
ΔGint-42 kcal/mol
Surface area19290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.000, 85.370, 63.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

21B-138-

HOH

DetailsThe biological assembly is a tetramer constructed from the AB dimer and a symmetry dimer generated by the two-fold.

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Components

#1: Protein TRANSTHYRETIN / TTR


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue fraction: PLASMA / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.12 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% PEG 550MME, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1drop
23 mg/mlprotein1drop
30.1 MHEPES1drop
440 %(w/v)PEG550 MME1drop
50.1 MHEPES1reservoir
640 %(w/v)PEG550 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 439563 / Num. obs: 38636 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.174 / Num. unique all: 2797 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 58852 / Num. measured all: 439563 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 95.7 % / Mean I/σ(I) obs: 9.6

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Individual anisotropic B-factor refinement as implemented in Refmac was performed. Reflections to 1.3A resolution (40% of total) are also included in the refinement. The completeness at 1.5A ...Details: Individual anisotropic B-factor refinement as implemented in Refmac was performed. Reflections to 1.3A resolution (40% of total) are also included in the refinement. The completeness at 1.5A is 97.9%. Crystals were grown at physiological pH. CNS was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4664 10 %Random
Rwork0.186 ---
all0.188 38636 --
obs0.188 46468 79.1 %-
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 0 186 1971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.809
X-RAY DIFFRACTIONx_improper_angle_d1.415
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg28
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.415
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.36 Å / Rfactor Rfree: 0.271 / Num. reflection Rfree: 290 / Rfactor Rwork: 0.252 / Num. reflection Rwork: 2983

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