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- PDB-1tz8: The monoclinic crystal structure of transthyretin in complex with... -

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Basic information

Entry
Database: PDB / ID: 1tz8
TitleThe monoclinic crystal structure of transthyretin in complex with diethylstilbestrol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloid / Transthyretin / Diethylstilbestrol / Protein stabilization
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
ACETATE ION / CARBONATE ION / DIETHYLSTILBESTROL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMorais-de-Sa, E.M. / Pereira, P.J.B. / Saraiva, M.J. / Damas, A.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The crystal structure of transthyretin in complex with diethylstilbestrol: a promising template for the design of amyloid inhibitors
Authors: Morais-de-Sa, E.M. / Pereira, P.J.B. / Saraiva, M.J. / Damas, A.M.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 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 / 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
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,29612
Polymers55,1094
Non-polymers1,1868
Water5,801322
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,10512
Polymers55,1094
Non-polymers9958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8610 Å2
ΔGint-53 kcal/mol
Surface area17990 Å2
MethodPISA, PQS
2
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2446
Polymers27,5552
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-52 kcal/mol
Surface area18830 Å2
MethodPISA
3
C: Transthyretin
D: Transthyretin
hetero molecules

C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,48712
Polymers55,1094
Non-polymers1,3788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)74.271, 96.961, 81.717
Angle α, β, γ (deg.)90.00, 107.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-129-

DES

21C-129-

DES

31D-128-

DES

41D-128-

DES

51A-4295-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 13777.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766

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Non-polymers , 6 types, 330 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DES / DIETHYLSTILBESTROL


Mass: 268.350 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H20O2
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.84 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Sodium Acetate (0.2M), Ammonium Sulfate (2.4M), glycerol (7%), 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: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.85→41.37 Å / Num. all: 46610 / Num. obs: 46580 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Rsym value: 0.053 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6709 / Rsym value: 0.21 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
ARPmodel building
WARPmodel building
CCP4(SCALA)data scaling
ARP/wARPV. 6.0model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F86

1f86


Resolution: 1.85→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2314 -Randomly selected subset of 5% of all reflections
Rwork0.195 ---
all0.198 46540 --
obs0.198 46540 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 84 322 3830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_deg1.326

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