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- PDB-1qwh: a covalent dimer of transthyretin that affects the amyloid pathway -

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Basic information

Entry
Database: PDB / ID: 1qwh
Titlea covalent dimer of transthyretin that affects the amyloid pathway
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / thyroid hormone / liver / plasma / cerebrospinal fluid / polyneuropathy / disease mutation / transport / thyroxine / binding protein / HORMONE-GROWTH FACTOR COMPLEX
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsFoss, T. / Kelker, M.S. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Kinetic stabilization of the native state by protein engineering: implications for inhibition of transthyretin amyloidogenesis.
Authors: Foss, T.R. / Kelker, M.S. / Wiseman, R.L. / Wilson, I.A. / Kelly, J.W.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THIS CONSTRUCT OF TRANSTHYRETIN WAS MADE BY JOINING TWO MONOMERS VIA A GLYCINE RICH ...SEQUENCE THIS CONSTRUCT OF TRANSTHYRETIN WAS MADE BY JOINING TWO MONOMERS VIA A GLYCINE RICH PEPTIDE TO ESSENTIALLY FORM A DIMER OF DIMERS, WHEN IN THE ACTIVE STATE. THE ACTIVE FORM OF THIS CONSTRUCT CRYSTALLIZED WITH HALF OF EACH FULL LENGTH DIMER IN THE ASYMMETRIC UNIT AND WAS ISOMORPHOUS WITH THE STRUCTURE OF 1BZD.PDB. NO ELECTRON DENSITY WAS OBSERVED FOR THE LINKER AND AS SUCH WAS REFINED AS TWO SEPERATE CHAINS (MONOMERS) IN THE ASYMMETRIC UNIT, AS FOR WILD TYPE TRANSTHYRETIN. THE SEQUENCE OF THE LINKER IS GSGGGTGGGSG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)25,7172
Polymers25,7172
Non-polymers00
Water2,252125
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)51,4334
Polymers51,4334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6210 Å2
ΔGint-44 kcal/mol
Surface area17570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.630, 86.050, 63.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 12858.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A linker, not seen in the density, was used to link chain A and B, see remark 999.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, 0.2 M Magnesium Nitrate , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2003
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. all: 48411 / Num. obs: 48411 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.053 / Net I/σ(I): 24.5
Reflection shellResolution: 1.36→29.88 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.539 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVQ.pdb

1dvq


Resolution: 1.36→29.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.914 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22246 2427 5 %RANDOM
Rwork0.21534 ---
obs0.21571 48380 92.34 %-
all-48411 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.855 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.36→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 0 125 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9342334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021273
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2655
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 166
Rwork0.252 3482

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