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- PDB-1gko: An Engineered Transthyretin Monomer that is Non-amyloidogenic - U... -

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Basic information

Entry
Database: PDB / ID: 1gko
TitleAn Engineered Transthyretin Monomer that is Non-amyloidogenic - Unless Partially Denatured
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT(THYROXINE) / TRANSTHYRETIN / TTR / MUTANT MONOMER TRANSTHYRETIN / MUTANT MONOMER TTR / AMYLOID FORMING PROTEIN / AMYLOID
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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/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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, X. / Smith, C.S. / Petrassi, H.M. / Hammarstrom, P. / White, J.T. / Sacchettini, J.C. / Kelly, J.W.
CitationJournal: Biochemistry / Year: 2001
Title: An Engineered Transthyretin Monomer that is Nonamyloidogenic, Unless It is Partially Denatured
Authors: Jiang, X. / Smith, C.S. / Petrassi, H.M. / Hammarstrom, P. / White, J.T. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionAug 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_assembly ...exptl_crystal_grow / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _exptl_crystal_grow.method / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)55,1184
Polymers55,1184
Non-polymers00
Water3,567198
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

C: TRANSTHYRETIN
D: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,1184
Polymers55,1184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area5930 Å2
ΔGint-49 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.729, 83.301, 86.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TRANSTHYRETIN / TBPA / TTR / ATTR


Mass: 13779.420 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION PHE87MET AND LEU130MET

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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: 2.4 Å3/Da / Density % sol: 41.6 %
Crystal growMethod: microbatch / pH: 8.8
Details: 0.2 M MGCL2, 0.1 M TRIS BUFFER, PH 8.5, 30% W/V POLYETHYLENE GLYCOL 4000
Crystal grow
*PLUS
Method: other / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
20.2 M1reservoirMgCl2
30.1 MTris1reservoirpH8.5
430 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: M / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→27.17 Å / Num. obs: 27827 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.4
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 1.5 / % possible all: 91.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMZ

1bmz


Resolution: 2.1→6 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -10 %RANDOM
Rwork0.2067 ---
obs0.2067 27291 98.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.17 Å20 Å2-
2--0 Å20 Å2
3---9.267 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 0 198 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2041.5
X-RAY DIFFRACTIONc_mcangle_it1.7962
X-RAY DIFFRACTIONc_scbond_it2.1772
X-RAY DIFFRACTIONc_scangle_it3.1132.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.15 Å
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rfree: 0.2755
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.54

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