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- PDB-1g1o: CRYSTAL STRUCTURE OF THE HIGHLY AMYLOIDOGENIC TRANSTHYRETIN MUTAN... -

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Basic information

Entry
Database: PDB / ID: 1g1o
TitleCRYSTAL STRUCTURE OF THE HIGHLY AMYLOIDOGENIC TRANSTHYRETIN MUTANT TTR G53S/E54D/L55S
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / Greek key / Beta barrel / beta-slip
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/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: 2.3 Å
AuthorsEneqvist, T. / Andersson, K. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
Citation
Journal: Mol.Cell / Year: 2000
Title: The beta-slip: a novel concept in transthyretin amyloidosis.
Authors: Eneqvist, T. / Andersson, K. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
#1: Journal: 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.
#2: Journal: Amyloid / Year: 1996
Title: The "edge strand" Hypothesis: Prediction and Test of a Mutational "hot-spot" on the Transthyretin Molecule Associated with FAP Amyloidogenesis
Authors: Serpell, L.C. / Goldsteins, G. / Dacklin, I. / Lundgren, E. / Blake, C.C.F.
#3: Journal: Biochemistry / Year: 1997
Title: Characterization of Two Highly Amyloidogenic Mutants of Transthyretin
Authors: Goldsteins, G. / Andersson, K. / Olofsson, A. / Dacklin, I. / Edvinsson, A. / Baranov, V. / Sandgren, O. / Thylen, C. / Hammarstrom, S. / Lundgren, E.
History
DepositionOct 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,0694
Polymers55,0694
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-41 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.310, 58.310, 228.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN


Mass: 13767.280 Da / Num. of mol.: 4 / Mutation: G53S,E54D,L55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.04 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 5000 MME, sodium citrate, ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
250 mMTris1drop
340-42 %PEG MME50001reservoir
4100 mMsodium citrate1reservoir
5100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 21080 / Num. obs: 20911 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2960 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. measured all: 109159
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 2960 / Num. measured obs: 14781

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 939 5 %Random
Rwork0.238 ---
all-20912 --
obs-19431 92.9 %-
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.7 Å2-4.9 Å20 Å2
2---9.7 Å20 Å2
3---19.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 0 143 3609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d27.14
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3725 91 5 %
Rwork0.3317 1563 -
obs--82.17 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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