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- PDB-5ttr: LEU 55 PRO TRANSTHYRETIN CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 5ttr
TitleLEU 55 PRO TRANSTHYRETIN CRYSTAL STRUCTURE
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT / TRANSTHYRETIN / AMYLOID / FAP / THYROXINE
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSebastiao, M.P. / Saraiva, M.J. / Damas, A.M.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: The crystal structure of amyloidogenic Leu55 --> Pro transthyretin variant reveals a possible pathway for transthyretin polymerization into amyloid fibrils.
Authors: Sebastiao, M.P. / Saraiva, M.J. / Damas, A.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Leu55Pro Variant Transthyretin
Authors: Sebastiao, P. / Dauter, Z. / Saraiva, M.J. / Damas, A.M.
#2: Journal: Biochemistry / Year: 1993
Title: Transthyretin Mutation Leu-55-Pro Significantly Alters Tetramer Stability and Increases Amyloidogenicity
Authors: Mccutchen, S.L. / Colon, W. / Kelly, J.W.
#3: Journal: Hum.Genet. / Year: 1992
Title: Transthyretin Pro55, a Variant Associated with Early-Onset, Aggressive, Diffuse Amyloidosis with Cardiac and Neurologic Involvement
Authors: Jacobson, D.R. / Mcfarlin, D.E. / Kane, I. / Buxbaum, J.N.
History
DepositionApr 30, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 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
E: TRANSTHYRETIN
F: TRANSTHYRETIN
G: TRANSTHYRETIN
H: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)110,0918
Polymers110,0918
Non-polymers00
Water00
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,0454
Polymers55,0454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
C: TRANSTHYRETIN
D: TRANSTHYRETIN
E: TRANSTHYRETIN
F: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,0454
Polymers55,0454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-41 kcal/mol
Surface area19710 Å2
MethodPISA
3
G: TRANSTHYRETIN
H: TRANSTHYRETIN

G: TRANSTHYRETIN
H: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,0454
Polymers55,0454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)149.990, 78.740, 98.950
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.597904, -0.003015, -0.801562), (-0.000247, -0.999992, 0.003947), (-0.801567, 0.002558, 0.597899)
Vector: 0.35072, 101.29226, -0.06993)

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN / TTR


Mass: 13761.317 Da / Num. of mol.: 8 / Mutation: L55P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contained 50:50 mixture of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
245 %satammonium sulfate1reservoir
37 %PEG4001reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.064
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 31394 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTA

1tta


Resolution: 2.7→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.199 --
obs-68168 98 %
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7147 0 0 0 7147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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