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- PDB-3dgd: Crystal structure of the F87M/L110M mutant of human transthyretin... -

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Basic information

Entry
Database: PDB / ID: 3dgd
TitleCrystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6
ComponentsTransthyretin
KeywordsLIGAND BINDING PROTEIN / TRANSTHYRETIN / MONOMER / AMYLOIDOGENIC INTERMEDIATE / ACIDIC PH / THYROID HORMONE BINDING PROTEIN
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 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.383 Å
AuthorsPalmieri, L.C. / Freire, J.B.B. / Foguel, D. / Lima, L.M.T.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition.
Authors: Palmieri, L.de.C. / Lima, L.M. / Freire, J.B. / Bleicher, L. / Polikarpov, I. / Almeida, F.C. / Foguel, D.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
SupersessionNov 3, 2010ID: 3CYK
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,08434
Polymers55,1184
Non-polymers1,96630
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-328 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.950, 60.690, 82.990
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13779.420 Da / Num. of mol.: 4 / Mutation: Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PLAB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 4,6; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, PH 4.6, ...Details: ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 4,6; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.305 / Wavelength: 1.305 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 1.383→83.045 Å / Num. all: 92482 / Num. obs: 92482 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.1
Reflection shellResolution: 1.383→1.46 Å / Redundancy: 7 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1 / Rsym value: 0.774 / % possible all: 94.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41 POLY ALA

1f41


Resolution: 1.383→19.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.391 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.202 5424 5.9 %RANDOM
Rwork0.157 ---
obs0.159 92475 97.2 %-
all-92482 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.07 Å2
2--0.35 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.383→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 81 374 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0214434
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.9486120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1255594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00224.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24215699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9851517
X-RAY DIFFRACTIONr_chiral_restr0.3110.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023583
X-RAY DIFFRACTIONr_nbd_refined0.2920.22180
X-RAY DIFFRACTIONr_nbtor_refined0.330.22996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2437
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3920.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4660.242
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2430.27
X-RAY DIFFRACTIONr_mcbond_it3.3751.52874
X-RAY DIFFRACTIONr_mcangle_it4.41624581
X-RAY DIFFRACTIONr_scbond_it5.71231831
X-RAY DIFFRACTIONr_scangle_it7.4174.51539
X-RAY DIFFRACTIONr_rigid_bond_restr3.81734705
X-RAY DIFFRACTIONr_sphericity_free14.6493415
X-RAY DIFFRACTIONr_sphericity_bonded9.16134284
LS refinement shellResolution: 1.383→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 392 -
Rwork0.233 6227 -
obs--94.9 %

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