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

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Entry
Database: PDB / ID: 1eta
TitleTHE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL 30-->MET 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
3,5,3',5'-TETRAIODO-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBraden, B.C. / Steinrauf, L.K. / Hamilton, J.A.
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: J.Biol.Chem. / Year: 1993
Title: X-Ray Crystal Structure of the Ala 109-->Thr Variant of Human Transthyretin which Produces Euthyroid Hyperthyroxinemia
Authors: Steinrauf, L.K. / Hamilton, J.A. / Braden, B.C. / Murrell, J.R. / Benson, M.D.
#2: 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.J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L.
History
DepositionMay 12, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Remark 700SHEET SHEET IDENTIFIERS ARE BASED ON ENTRY 2PAB (PREALBUMIN, BLAKE ET AL.). A SHIFT OF THE CHAIN 1 ...SHEET SHEET IDENTIFIERS ARE BASED ON ENTRY 2PAB (PREALBUMIN, BLAKE ET AL.). A SHIFT OF THE CHAIN 1 AND 2 BETA SHEETS AT RESIDUE 30 WAS NECESSARY TO MODEL THE MET SIDE CHAIN. BETA SHEET MAIN CHAIN CONNECTIVITIES IN THE COORDINATE SET ARE TO THE VAL 30 PEPTIDE ATOMS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: TRANSTHYRETIN
2: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1734
Polymers27,6192
Non-polymers1,5542
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area12360 Å2
MethodPISA
2
1: TRANSTHYRETIN
2: TRANSTHYRETIN
hetero molecules

1: TRANSTHYRETIN
2: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3458
Polymers55,2384
Non-polymers3,1074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9640 Å2
ΔGint-34 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.640, 86.180, 65.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: THIS IS A NATURALLY OCCURRING VARIANT WITH MICROHETEROGENEITY AT POSITION 30. BOTH VAL AND MET OCCUR AT THIS POSITION. THE RATIO OF MET VAL AT POSITION 30 IS 1:1 AND BOTH VAL AND MET ARE MODELLED WITH 0.50 OCCUPANCY.
Components on special symmetry positions
IDModelComponents
112-241-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9886, 0.1508, -0.0004), (0.1508, 0.9886, -0.0049), (-0.0004, -0.0049, -0.9999)
Vector: 36.751, -2.55, 98.39)
DetailsTHERE ARE TWO T4 BINDING SITES PER TETRAMER (AA, BB). SITE AA CONTAINS RESIDUES FROM CHAIN 1 AND CHAIN 1* WHERE CHAINS 1 AND 1* ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY. LIKEWISE, SITE BB CONTAINS RESIDUES FROM CHAIN 2 AND CHAIN 2* WHERE CHAINS 2 AND 2* ARE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. BECAUSE OF PDB FORMAT SPECIFICATIONS, ONLY THE RESIDUES FROM CHAIN 1 ARE LISTED FOR SITE AA ON SITE RECORDS BELOW AND ONLY THE RESIDUES FROM CHAIN 2 ARE LISTED FOR SITE BB ON SITE RECORDS BELOW. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 2 WHEN APPLIED TO CHAIN 1.

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Components

#1: Protein TRANSTHYRETIN


Mass: 13809.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P02766
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 45.02 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å / Rfactor obs: 0.184 / σ(F): 2
Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED ...Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF .001 HAVE NO OBSERVABLE ELECTRON DENSITY. SOME WATER MOLECULES WERE PLACED IN POSITIONS THAT PROBABLY REPRESENT ALTERNATE CONFORMATIONS.
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 48 236 2274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.027

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