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- PDB-1ttc: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -

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Basic information

Entry
Database: PDB / ID: 1ttc
TitleTHE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL30MET VARIANT TO 1.7 ANGSTROMS RESOLUTION
ComponentsTransthyretin
KeywordsTRANSPORT(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) / 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 / Resolution: 1.7 Å
AuthorsHamilton, J.A. / Steinrauf, L.K. / Braden, B.C.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution.
Authors: Hamilton, J.A. / Steinrauf, L.K. / Braden, B.C. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L.
#1: Journal: Biochim.Biophys.Acta / Year: 1992
Title: Alteration in Molecular Structure which Results in Disease: The met-30 Variant of Human Plasma Transthyretin
Authors: Hamilton, J.A. / Steinrauf, L.K. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L.
History
DepositionNov 2, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,6192
Polymers27,6192
Non-polymers00
Water5,747319
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,2384
Polymers55,2384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6230 Å2
ΔGint-47 kcal/mol
Surface area21350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.010, 86.290, 65.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: GLU B 7 - SER B 8 149.677 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO B 102
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98909, 0.14667, 0.01379), (0.14696, 0.98887, 0.02306), (-0.01026, 0.02484, -0.99964)
Vector: 36.39515, -3.40894, 98.11504)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13809.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Organ: PLASMA / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
240 %ammonium sulfate1reservoir
3200 mMcitrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 25770 / Rmerge(I) obs: 0.063

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5.8 Å / Rfactor obs: 0.179 / σ(F): 2
Details: OCCUPANCIES OF DISORDERED SIDE CHAINS AND ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED ON THE BASIS OF DIFFERENCE FOURIER MAPS. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ...Details: OCCUPANCIES OF DISORDERED SIDE CHAINS AND ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED ON THE BASIS OF DIFFERENCE FOURIER MAPS. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ELECTRON DENSITY. OCCUPANCIES OF SOLVENT MOLECULES WERE REFINED WITH PROLSQ. A NUMBER OF WATER MOLECULE SITES WHICH ARE ONLY PARTIALLY OCCUPIED WERE INCLUDED IN THIS STRUCTURE. BECAUSE OF THIS, SHORT CONTACT DISTANCES ARE FOUND BETWEEN SOME OF THESE WATER MOLECULES.
Refinement stepCycle: LAST / Resolution: 1.7→5.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 0 319 2265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
Software
*PLUS
Name: 'PROTIN and PROLSQ' / Classification: refinement
Refinement
*PLUS
Num. reflection all: 19860
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.040.038
X-RAY DIFFRACTIONp_plane_restr0.020.013
X-RAY DIFFRACTIONp_chiral_restr0.150.166
X-RAY DIFFRACTIONp_mcbond_it10.745
X-RAY DIFFRACTIONp_scbond_it10.665
X-RAY DIFFRACTIONp_mcangle_it1.51.34
X-RAY DIFFRACTIONp_scangle_it1.51.186

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