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- PDB-1oo2: Crystal structure of transthyretin from Sparus aurata -

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Basic information

Entry
Database: PDB / ID: 1oo2
TitleCrystal structure of transthyretin from Sparus aurata
Componentstransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / retinol-binding protein / tetramer
Function / homology
Function and homology information


thyroid hormone binding / purine nucleobase metabolic process / hormone activity / response to estrogen / extracellular region
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / 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
: / Transthyretin / Transthyretin
Similarity search - Component
Biological speciesSparus aurata (gilthead seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPasquato, N. / Ramazzina, I. / Folli, C. / Battistutta, R. / Berni, R. / Zanotti, G.
Citation
Journal: Febs Lett. / Year: 2003
Title: Distinctive binding and structural properties of piscine transthyretin.
Authors: Folli, C. / Pasquato, N. / Ramazzina, I. / Battistutta, R. / Zanotti, G. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: A comparative analysis of 23 structures of the amyloidogenic protein transthyretin
Authors: Hornberg, A. / Eneqvist / T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
#2: Journal: Science / Year: 1995
Title: Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein
Authors: Monaco, H.L. / Rizzi, M. / Coda, A.
#3: Journal: Biochemistry / Year: 1999
Title: The structure of human retinol-binding protein (RBP) with its carrier protein transthyretin reveals an interaction with the carboxy terminus of RBP
Authors: Naylor, H. / Newcomer, M.E.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
C: transthyretin
D: transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5386
Polymers51,3134
Non-polymers2252
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-56 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.452, 65.622, 70.834
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-100-

GLU

21A-208-

HOH

DetailsTHE TETRAMER IN THE ASYMMETRIC UNIT is the biological assembly

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Components

#1: Protein
transthyretin


Mass: 12828.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sparus aurata (gilthead seabream) / Gene: TTR / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: O93330, UniProt: Q9PTT3*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 400, cadmio chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1reservoirCaCl2
250 mMsodium acetate1reservoir
315 %(w/v)PEG4001reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2003
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.559→50 Å / Num. all: 60660 / Num. obs: 60660 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7 / Num. unique all: 7334 / Rsym value: 0.146 / % possible all: 89.9
Reflection
*PLUS
Highest resolution: 1.56 Å / Lowest resolution: 48 Å / Num. measured all: 239286
Reflection shell
*PLUS
% possible obs: 89.9 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.56→10 Å / Num. parameters: 15579 / Num. restraintsaints: 14689 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 6040 11.1 %RANDOM
Rwork0.1973 ---
all0.203 54369 --
obs0.1973 54369 87.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3891
Refinement stepCycle: LAST / Resolution: 1.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 2 365 3883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.077
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.56→1.64 Å /
RfactorNum. reflection
Rwork0.221 -
obs-7045
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 48 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.056

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