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- PDB-1tfp: TRANSTHYRETIN (FORMERLY KNOWN AS PREALBUMIN) -

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Basic information

Entry
Database: PDB / ID: 1tfp
TitleTRANSTHYRETIN (FORMERLY KNOWN AS PREALBUMIN)
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT (THYROXINE) / ALBUMIN / RETINOL-BINDING
Function / homology
Function and homology information


yolk / oocyte growth / thyroid hormone binding / thyroid hormone transport / clathrin-coated vesicle / retinol metabolic process / small molecule binding / hormone binding / protein tetramerization / hormone activity ...yolk / oocyte growth / thyroid hormone binding / thyroid hormone transport / clathrin-coated vesicle / retinol metabolic process / small molecule binding / hormone binding / protein tetramerization / hormone activity / response to virus / protein-containing complex assembly / protein heterodimerization activity / protein domain specific binding / protein-containing complex / extracellular space
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsSunde, M. / Richardson, S.J. / Chang, L. / Pettersson, T.M. / Schreiber, G. / Blake, C.C.F.
Citation
Journal: Eur.J.Biochem. / Year: 1996
Title: The crystal structure of transthyretin from chicken.
Authors: Sunde, M. / Richardson, S.J. / Chang, L. / Pettersson, T.M. / Schreiber, G. / Blake, C.C.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: Structure of Prealbumin: Secondary, Tertiary and Quaternary Interactions Determined by Fourier Refinement at 1.8 A
Authors: Blake, C.C. / Geisow, M.J. / Oatley, S.J. / Rerat, B. / Rerat, C.
History
DepositionJan 5, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4473
Polymers28,3512
Non-polymers961
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-5 kcal/mol
Surface area11050 Å2
MethodPISA
2
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8956
Polymers56,7034
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area6840 Å2
ΔGint-37 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 77.660, 161.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6091, -0.6784, -0.4108), (-0.6763, 0.1739, 0.7158), (-0.4141, 0.7139, -0.5647)
Vector: 11.4548, -0.6954, 11.3033)

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Components

#1: Protein TRANSTHYRETIN / PREALBUMIN


Mass: 14175.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: SERUM / References: UniProt: P27731
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.47 Å3/Da / Density % sol: 62 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21 mMEDTA1drop
30.02 %sodium azide1drop
40.5 Mlithium sulfate1reservoir
520 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 10781 / % possible obs: 78 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Num. measured all: 22739

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.9→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.199 --
obs0.199 24699 86.8 %
Displacement parametersBiso mean: 52.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 1 1 1772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.677
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.422
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.422

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