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

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Basic information

Entry
Database: PDB / ID: 3did
TitleCrystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6 soaked
ComponentsTransthyretin
KeywordsLIGAND BINDING PROTEIN / TRANSTHYRETIN / MONOMER / AMYLOIDOGENIC INTERMEDIATE / ACIDIC PH / THYROID HORMONE BINDING PROTEIN
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
ACETATE ION / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)56,44124
Polymers55,1184
Non-polymers1,32320
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-438 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.030, 63.470, 48.670
Angle α, β, γ (deg.)90.00, 90.00, 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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
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 4.60, ...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 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.78→86.066 Å / Num. all: 48268 / Num. obs: 48266 / % possible obs: 96.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 6.6
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.5 / Num. measured all: 21553 / Num. unique all: 6857 / Rsym value: 0.506 / % possible all: 93.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å28.74 Å
Translation3.5 Å28.74 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→86.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.827 / SU B: 6.627 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2711 5.6 %RANDOM
Rwork0.181 ---
obs0.185 48266 95.78 %-
all-48268 --
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 max: 93.33 Å2 / Biso mean: 43.545 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.02 Å2
2--0.44 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.78→86.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 48 287 3893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0213988
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.9375481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2325519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71723.704162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951516
X-RAY DIFFRACTIONr_chiral_restr0.20.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023120
X-RAY DIFFRACTIONr_nbd_refined0.2520.21166
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.2174
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.28
X-RAY DIFFRACTIONr_mcbond_it2.6161.52752
X-RAY DIFFRACTIONr_mcangle_it3.524098
X-RAY DIFFRACTIONr_scbond_it5.37631691
X-RAY DIFFRACTIONr_scangle_it6.3634.51383
X-RAY DIFFRACTIONr_rigid_bond_restr4.64934443
X-RAY DIFFRACTIONr_sphericity_free11.1083319
X-RAY DIFFRACTIONr_sphericity_bonded7.5633862
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 198 -
Rwork0.25 3237 -
all-3435 -
obs--92.96 %

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