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- PDB-2pab: STRUCTURE OF PREALBUMIN, SECONDARY, TERTIARY AND QUATERNARY INTER... -

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Basic information

Entry
Database: PDB / ID: 2pab
TitleSTRUCTURE OF PREALBUMIN, SECONDARY, TERTIARY AND QUATERNARY INTERACTIONS DETERMINED BY FOURIER REFINEMENT AT 1.8 ANGSTROMS
ComponentsTRANSTHYRETIN PRECURSOR
KeywordsTRANSPORT (THYROXINE / RETINOL) IN SERUM
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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: 1.8 Å
AuthorsOatley, S.J. / Blake, C.C.F.
Citation
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.
#1: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin,A Model of the Thyroid Hormone Nuclear Receptor (Query)
Authors: Blake, C.C.F. / Oatley, S.J.
#2: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Human Plasma Prealbumin at 2.5 Angstroms Resolution,A Preliminary Report on the Polypeptide Chain Conformation,Quaternary Structure and Thyroxine Binding
Authors: Blake, C.C.F. / Geisow, M.J. / Swan, I.D.A. / Rerat, C. / Rerat, B.
#3: Journal: J.Mol.Biol. / Year: 1971
Title: An X-Ray Study of the Subunit Structure of Prealbumin
Authors: Blake, C.C.F. / Swan, I.D.A. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B.
#4: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#5: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionSep 16, 1977Processing site: BNL
SupersessionOct 24, 1977ID: 1PAB
Revision 1.0Oct 24, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 700SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMODATE ...SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMODATE THESE DISCONTINUITIES EACH *EXTERNAL* SHEET IS REPRESENTED HERE TWICE, WITH A DIFFERENT STRAND 1 IN EACH CASE. STRANDS 2,3,4 OF *X1A* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2A*. SIMILARLY STRANDS 2,3,4 OF *X1B* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2B*. DESPITE THIS PARTIAL REDUNDANCY OF REPRESENTATION THERE IS NO IMPLICATION THAT EACH SUBUNIT CONTAINS MORE THAN ONE *EXTERNAL* SHEET SUBSTRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSTHYRETIN PRECURSOR
B: TRANSTHYRETIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)27,5532
Polymers27,5532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
2
A: TRANSTHYRETIN PRECURSOR
B: TRANSTHYRETIN PRECURSOR

A: TRANSTHYRETIN PRECURSOR
B: TRANSTHYRETIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)55,1064
Polymers55,1064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6170 Å2
ΔGint-47 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.490, 85.680, 65.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-0.98771, 0.156297), (0.156297, 0.98771), (-1) / Vector: 36.52699, -2.87217, 32.995)
DetailsTHIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC DIAD PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM, I. E. XPRIME=-X, YPRIME=-Y, ZPRIME=Z.

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Components

#1: Protein TRANSTHYRETIN PRECURSOR


Mass: 13776.376 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02766

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal grow
*PLUS
Method: other / Details: Blake, C.C.F., (1974) J. Mol. Biol., 88, 1.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→15 Å

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Processing

RefinementResolution: 1.8→8 Å / Rfactor Rwork: 0.29 / Rfactor obs: 0.29
Details: THE AXES OF THE COORDINATE SYSTEM USED HERE ARE ALIGNED WITH THE CRYSTALLOGRAPHIC AXES BUT THE ORIGIN IS DISPLACED BY A/2, B/2, C/4 AS GIVEN IN THE SCALE RECORDS BELOW.
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 0 1744
Refinement
*PLUS
Rfactor obs: 0.289
Solvent computation
*PLUS
Displacement parameters
*PLUS

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