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- PDB-2qgd: Human transthyretin (TTR) complexed with 2-(3,5-Dibromo-4-hydroxy... -

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Basic information

Entry
Database: PDB / ID: 2qgd
TitleHuman transthyretin (TTR) complexed with 2-(3,5-Dibromo-4-hydroxyphenyl)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) / 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
4-(1,3-BENZOXAZOL-2-YL)-2,6-DIBROMOPHENOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)28,2934
Polymers27,5552
Non-polymers7382
Water2,558142
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5858
Polymers55,1094
Non-polymers1,4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8690 Å2
ΔGint-61 kcal/mol
Surface area18590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.945, 85.001, 65.097
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-200-

MR5

21A-200-

MR5

31A-200-

MR5

41A-200-

MR5

51B-201-

MR5

61B-201-

MR5

71B-201-

MR5

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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-MR5 / 4-(1,3-BENZOXAZOL-2-YL)-2,6-DIBROMOPHENOL / 2-(3,5-DIBROMO-4-HYDROXYPHENYL)BENZOXAZOLE


Mass: 369.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H7Br2NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 42.91 %
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: 0.912 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)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionRedundancy: 14.5 % / Av σ(I) over netI: 11 / Number: 557366 / Rmerge(I) obs: 0.062 / Χ2: 1.05 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 38438 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.75098.810.0330.99713.2
2.943.710010.0381.03214.1
2.562.9410010.050.98814.5
2.332.5610010.0631.04114.7
2.162.3310010.0660.99614.7
2.042.1610010.0771.06514.7
1.932.0410010.0931.05614.7
1.851.9310010.1221.1114.7
1.781.8510010.1821.08414.7
1.721.7810010.2481.08414.7
1.661.7210010.3131.08714.7
1.621.6610010.3751.06414.6
1.571.6210010.4411.06514.6
1.531.5710010.5411.05714.6
1.51.5310010.671.04714.5
ReflectionResolution: 1.5→50 Å / Num. obs: 38438 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.062 / Χ2: 1.052 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2511 / Rsym value: 0.67 / 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: 1.5→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.188 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1924 5 %RANDOM
Rwork0.16 ---
obs0.162 38380 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 36 142 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221973
X-RAY DIFFRACTIONr_bond_other_d0.0030.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9682718
X-RAY DIFFRACTIONr_angle_other_deg0.9323.0013171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06723.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4121510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.1990.2325
X-RAY DIFFRACTIONr_nbd_other0.2030.21248
X-RAY DIFFRACTIONr_nbtor_refined0.180.2922
X-RAY DIFFRACTIONr_nbtor_other0.0880.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.212
X-RAY DIFFRACTIONr_mcbond_it2.5211.51549
X-RAY DIFFRACTIONr_mcbond_other0.9251.5482
X-RAY DIFFRACTIONr_mcangle_it3.0221967
X-RAY DIFFRACTIONr_scbond_it4.4193945
X-RAY DIFFRACTIONr_scangle_it5.3854.5736
X-RAY DIFFRACTIONr_rigid_bond_restr2.28234113
X-RAY DIFFRACTIONr_sphericity_free9.9743142
X-RAY DIFFRACTIONr_sphericity_bonded4.78233203
LS refinement shellResolution: 1.5→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 122 -
Rwork0.15 2491 -
obs-2613 92.53 %

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