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- PDB-2g9k: Human Transthyretin (TTR) Complexed with Hydroxylated polychlorin... -

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Basic information

Entry
Database: PDB / ID: 2g9k
TitleHuman Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-2',3,3',4',5-Pentachlorobiphenyl
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / TTR / AMYLOID / TRANSTHYRETIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase 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
2',3,3',4',5-PENTACHLOROBIPHENYL-4-OL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPalaninathan, S.K. / Smith, C. / Safe, S.H. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: Chem.Biol. / Year: 2004
Title: Hydroxylated polychlorinated biphenyls selectively bind transthyretin in blood and inhibit amyloidogenesis: rationalizing rodent PCB toxicity
Authors: Purkey, H.E. / Palaninathan, S.K. / Kent, K.C. / Smith, C. / Safe, S.H. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_special_symmetry / 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)28,2404
Polymers27,5552
Non-polymers6852
Water91951
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4798
Polymers55,1094
Non-polymers1,3704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8720 Å2
ΔGint-152 kcal/mol
Surface area17810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.081, 85.461, 64.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

NE1

21A-501-

NE1

31A-501-

NE1

41A-501-

NE1

51A-501-

NE1

61A-501-

NE1

71B-500-

NE1

81B-500-

NE1

91B-500-

NE1

101B-500-

NE1

111B-500-

NE1

121B-500-

NE1

131A-295-

HOH

141B-294-

HOH

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Components

#1: Protein Transthyretin / / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-NE1 / 2',3,3',4',5-PENTACHLOROBIPHENYL-4-OL


Mass: 342.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H5Cl5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALLIZATION CONDITIONS: CRYSTALS OF RECOMBINANT WT TTR WERE OBTAINED FROM PROTEIN SOLUTIONS AT 5 MG/ML (IN 100 MM KCL, 100 MM PHOSPHATE [PH 7.4], 1 M AMMONIUM SULFATE) EQUILIBRATED ...Details: CRYSTALLIZATION CONDITIONS: CRYSTALS OF RECOMBINANT WT TTR WERE OBTAINED FROM PROTEIN SOLUTIONS AT 5 MG/ML (IN 100 MM KCL, 100 MM PHOSPHATE [PH 7.4], 1 M AMMONIUM SULFATE) EQUILIBRATED AGAINST 2 M AMMONIUM SULFATE IN HANGING DROP EXPERIMENTS. THE TTR LIGAND COMPLEXES WERE PREPARED FROM CRYSTALS SOAKED FOR 2 WEEKS WITH A 10-FOLD MOLAR EXCESS , pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 31, 1999
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→27.42 Å / Num. all: 18746 / Num. obs: 18746 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036
Reflection shellResolution: 1.85→1.898 Å / % possible all: 87.52

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMZ

1bmz


Resolution: 1.85→27.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.647 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25745 959 5.1 %RANDOM
Rwork0.21375 ---
all0.21586 18746 --
obs0.21586 17787 89.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 36 51 1857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9622573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34723.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.815291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.689158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0350.021418
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.3694
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.51291
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.374
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7960.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2531.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82321879
X-RAY DIFFRACTIONr_scbond_it2.6463953
X-RAY DIFFRACTIONr_scangle_it3.9244.5694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 81 -
Rwork0.268 1244 -
obs--87.52 %

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