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- PDB-2qge: Human transthyretin (TTR) complexed with 2-(3,5-Dimethylphenyl)be... -

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Basic information

Entry
Database: PDB / ID: 2qge
TitleHuman transthyretin (TTR) complexed with 2-(3,5-Dimethylphenyl)benzoxazole
ComponentsTransthyretin
KeywordsHormone/Growth Factor / Transthyretin / Tetramer / Amyloidogenesis Inhibitors / 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) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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-(3,5-DIMETHYLPHENYL)-1,3-BENZOXAZOLE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Biochemical and structural evaluation of highly selective 2-arylbenzoxazole-based transthyretin amyloidogenesis inhibitors.
Authors: Johnson, S.M. / Connelly, S. / Wilson, I.A. / Kelly, J.W.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)28,0014
Polymers27,5552
Non-polymers4472
Water2,666148
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0038
Polymers55,1094
Non-polymers8934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8580 Å2
ΔGint-75 kcal/mol
Surface area18650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.917, 85.777, 64.563
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
11B-200-

MR6

21A-276-

HOH

31B-273-

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: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-MR6 / 2-(3,5-DIMETHYLPHENYL)-1,3-BENZOXAZOLE


Mass: 223.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.36 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method. Crystals ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 11.8 / Number: 294859 / Rmerge(I) obs: 0.04 / Χ2: 1 / D res high: 1.45 Å / D res low: 50 Å / Num. obs: 42964 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.125099.210.0181.056.6
2.483.1210010.0260.9226.9
2.172.4810010.0380.9816.9
1.972.1710010.0520.97
1.831.9710010.0840.9796.9
1.721.8310010.151.0076.9
1.631.7210010.2231.0176.8
1.561.6310010.2851.0367
1.51.5610010.4151.0356.8
1.451.510010.5671.0476.8
ReflectionResolution: 1.45→50 Å / Num. obs: 42964 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.04 / Χ2: 0.997 / Net I/σ(I): 11.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 4242 / Rsym value: 0.567 / Χ2: 1.047 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Transthyretin PDB 2FBR

2fbr


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.064 / SU ML: 0.037 / Isotropic thermal model: Aniostropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2163 5 %RANDOM
Rwork0.164 ---
obs0.166 42922 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 34 148 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222009
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9682774
X-RAY DIFFRACTIONr_angle_other_deg1.0283.0013267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41624.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2881510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_nbd_refined0.2220.2333
X-RAY DIFFRACTIONr_nbd_other0.2120.21289
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2972
X-RAY DIFFRACTIONr_nbtor_other0.090.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.215
X-RAY DIFFRACTIONr_mcbond_it2.4841.51580
X-RAY DIFFRACTIONr_mcbond_other0.9471.5488
X-RAY DIFFRACTIONr_mcangle_it3.0422004
X-RAY DIFFRACTIONr_scbond_it4.1223952
X-RAY DIFFRACTIONr_scangle_it5.4754.5747
X-RAY DIFFRACTIONr_rigid_bond_restr2.10334183
X-RAY DIFFRACTIONr_sphericity_free10.7133150
X-RAY DIFFRACTIONr_sphericity_bonded4.63733266
LS refinement shellResolution: 1.45→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 182 -
Rwork0.161 2926 -
obs-3108 99.49 %

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