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

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Basic information

Entry
Database: PDB / ID: 1ttb
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


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase 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
AuthorsSteinrauf, L.K. / Hamilton, J.A. / 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 / 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)27,6152
Polymers27,6152
Non-polymers00
Water3,153175
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,2304
Polymers55,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6380 Å2
ΔGint-45 kcal/mol
Surface area21160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.720, 86.090, 65.790
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-610-

HOH

21B-618-

HOH

31B-619-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99042, 0.13799, -0.00439), (0.138, 0.99043, -0.00262), (0.00399, -0.00321, -0.99999)
Vector: 37.60101, -2.39622, 98.62653)
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: 13807.387 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 / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
238 %ammonium sulfate1reservoir
3100 mMsodium citrate1reservoir

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å / Rfactor obs: 0.157 / 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).
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 175 2123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.5
Software
*PLUS
Name: 'PROTIN and PROLSQ' / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18320
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_d0.040.029
X-RAY DIFFRACTIONp_plane_restr0.020.005
X-RAY DIFFRACTIONp_mcbond_it10.668
X-RAY DIFFRACTIONp_scbond_it1.50.914
X-RAY DIFFRACTIONp_mcangle_it1.51.186
X-RAY DIFFRACTIONp_scangle_it21.444

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