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

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Basic information

Entry
Database: PDB / ID: 1tta
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.
CitationJournal: 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.
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 1.3Nov 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 1.4Feb 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,5552
Polymers27,5552
Non-polymers00
Water3,315184
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 area6220 Å2
ΔGint-45 kcal/mol
Surface area21250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.800, 86.220, 65.780
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-786-

HOH

21A-789-

HOH

31B-787-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98814, 0.15334, -0.00848), (0.15341, 0.98814, -0.00727), (0.00727, -0.00848, -0.99994)
Vector: 37.08947, -2.45297, 98.68945)
DetailsMONOMERS A AND B OF THE DIMER ARE RELATED TO EACH OTHER BY A PSEUDO TWO-FOLD AXIS APPROXIMATELY PARALLEL TO THE CRYSTALLOGRAPHIC 'B' DIRECTION, PERPENDICULAR TO THE SURFACE OF THE SHEETS, AND PASSING BETWEEN THE H STRAND OF ONE MONOMER AND THE H STRAND OF THE OTHER. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. TWO AB DIMERS ARE ROTATED AROUND THE TWO-FOLD CRYSTALLOGRAPHIC AXIS TO FORM THE TETRAMER, AB-A'B'.

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Components

#1: Protein TRANSTHYRETIN


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 45.39 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion / pH: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2200 mMcitrate1reservoir
310 mg/mlprotein1reservoir
440 %ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Num. all: 26178 / Rmerge(I) obs: 0.053

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å / σ(F): 2
Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC ...Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ELECTRON DENSITY. SHEET IDENTIFIERS ARE BASED ON PROTEIN DATA BANK ENTRY 2PAB (PREALBUMIN, OATLEY AND BLAKE)
RfactorNum. reflection
obs0.168 19882
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 0 184 2127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.5
Software
*PLUS
Name: prolsq / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 5 Å / Num. reflection obs: 19882 / σ(F): 2 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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