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- PDB-1kgj: Rat transthyretin (also called prealbumin) complex with 3',5'-dib... -

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Basic information

Entry
Database: PDB / ID: 1kgj
TitleRat transthyretin (also called prealbumin) complex with 3',5'-dibromoflavone (EMD21388)
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / PREALBUMIN / TRANSPORT / DIBROMOFLAVONE / AURONE / THYROID HORMONE
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / 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
6,4'-DIHYDROXY-3-METHYL-3',5'-DIBROMOFLAVONE / Transthyretin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsWojtczak, A. / Neumann, P. / Muziol, T. / Cody, V. / Luft, J.R. / Pangborn, W.
Citation
Journal: Acta Biochim.Pol. / Year: 2001
Title: Comparison of binding interactions of dibromoflavonoids with transthyretin.
Authors: Muziol, T. / Cody, V. / Wojtczak, A.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex
Authors: Wojtczak, A. / Luft, J.R. / Cody, V.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin
Authors: Wojtczak, A. / Luft, J. / Cody, V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structures of Human Transthyretin Complexed with Thyroxine at 2.0 A Resolution and 3',5'-Dinitro-N-Acetyl-L-Thyronine at 2.2 A Resolution
Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of New Polymorphic Monoclinic Form of Hum Transthyretin at 3A Resolution Reveals a Mixed Comp between Unliganded and T4-Bound Tetramers of Ttr
Authors: Wojtczak, A. / Neumann, P. / Cody, V.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: STRUCTURE OF RAT (rTTR) TRANSTHYRETIN COMPLEX WITH THYROXINE AT 2.5 A RESOLUTION: FIRST NON-BIASED INS INTO THYROXINE BINDING REVEALS DIFFERENT HORMONE ORIENTATION IN TWO BINDING SITES
Authors: Wojtczak, A. / Cody, V. / Luft, J. / Pangborn, W.
History
DepositionNov 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / software / 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
C: TRANSTHYRETIN
D: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3096
Polymers54,4574
Non-polymers8522
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-43 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.545, 82.545, 161.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
TRANSTHYRETIN / Prealbumin / TBPA


Mass: 13614.147 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: plasma / References: UniProt: P02767
#2: Chemical ChemComp-FL8 / 6,4'-DIHYDROXY-3-METHYL-3',5'-DIBROMOFLAVONE


Mass: 426.056 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10Br2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.46 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulphate, acetate buffer, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
155-65 %ammonium sulfate1reservoir
20.1 Macetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→82.5 Å / Num. obs: 23846 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.86 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.1023 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.57 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / Num. unique all: 886 / % possible all: 81.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 82.5 Å

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Processing

Software
NameVersionClassification
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: TETRAMER OF RAT TTR, PDB ENTRY 1GKE

1gke


Resolution: 2.3→12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 191939.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: ENGH & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.288 793 4.9 %RANDOM
Rwork0.203 ---
all0.207 23613 --
obs0.207 16330 64.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.8207 Å2 / ksol: 0.27996 e/Å3
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 66 186 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it13.082
X-RAY DIFFRACTIONc_scangle_it11.992.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.407 36 4.2 %
Rwork0.342 850 -
obs-886 31.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAMETER2.INPTOPOLOGY2.INP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 12 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.296
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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