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- PDB-2b16: The crystal structure of 2,4-dinitrophenol in complex with the am... -

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Basic information

Entry
Database: PDB / ID: 2b16
TitleThe crystal structure of 2,4-dinitrophenol in complex with the amyloidogenic variant Transthyretin Tyr78Phe
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / 2 / 4-dinitrophenol / amyloid / tetramer stabilizer
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
2,4-DINITROPHENOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMorais-de-Sa, E. / Neto-Silva, R.M. / Pereira, P.J. / Saraiva, M.J. / Damas, A.M.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: The binding of 2,4-dinitrophenol to wild-type and amyloidogenic transthyretin
Authors: Morais-de-Sa, E. / Neto-Silva, R.M. / Pereira, P.J. / Saraiva, M.J. / Damas, A.M.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8914
Polymers27,5232
Non-polymers3682
Water2,774154
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7828
Polymers55,0454
Non-polymers7364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7810 Å2
ΔGint-63 kcal/mol
Surface area17610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.542, 85.869, 63.603
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-128-

DNF

21A-128-

DNF

31A-128-

DNF

41A-128-

DNF

51B-128-

DNF

61B-128-

DNF

71B-128-

DNF

81B-128-

DNF

91B-2154-

HOH

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Components

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


Mass: 13761.360 Da / Num. of mol.: 2 / Mutation: Y78F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pINTR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766
#2: Chemical ChemComp-DNF / 2,4-DINITROPHENOL


Mass: 184.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.22 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Ammonium Sulfate, glycerol, sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.748→38.069 Å / Num. all: 23470 / Num. obs: 23470 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3331 / Rsym value: 0.205 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
ARP/wARP6model building
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1F86

1f86


Resolution: 1.75→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1196 -Random
Rwork0.19 ---
all0.191 23350 --
obs0.191 23350 97.39 %-
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 26 154 1861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.337

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