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

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Basic information

Entry
Database: PDB / ID: 3gps
TitleCrystal structure of the F87M/L110M mutant of human transthyretin at pH 5.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / Amyloid / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Neuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A / Ligand 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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: 1.78 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
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 1.3Sep 6, 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)57,13833
Polymers55,1184
Non-polymers2,02029
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-454 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.495, 61.615, 47.268
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe tetramer in the AU is the biological molecule.

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Components

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


Mass: 13779.420 Da / Num. of mol.: 4 / Fragment: UNP residues 21 to 147 / Mutation: F87M,L110M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / 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


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, pH 5.5, VAPOR ...Details: ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, pH 5.5, 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: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.78→27.9 Å / Num. obs: 45854 / % possible obs: 99.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 8.1
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3 / Num. unique all: 6075 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0059refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DGD

3dgd


Resolution: 1.78→27.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.502 / SU ML: 0.105 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 2697 5.9 %RANDOM
Rwork0.20205 ---
all0.2023 ---
obs0.20508 43051 99.18 %-
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: 28.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.58 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.78→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 94 205 3850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224062
X-RAY DIFFRACTIONr_bond_other_d0.0020.022643
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9525563
X-RAY DIFFRACTIONr_angle_other_deg1.01636480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7825522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89223.81168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96215630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8881519
X-RAY DIFFRACTIONr_chiral_restr0.1170.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214658
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02825
X-RAY DIFFRACTIONr_mcbond_it1.6921.52536
X-RAY DIFFRACTIONr_mcbond_other0.7731.5988
X-RAY DIFFRACTIONr_mcangle_it2.69924128
X-RAY DIFFRACTIONr_scbond_it3.50631526
X-RAY DIFFRACTIONr_scangle_it5.2534.51435
X-RAY DIFFRACTIONr_rigid_bond_restr1.89536705
X-RAY DIFFRACTIONr_sphericity_free9.7723236
X-RAY DIFFRACTIONr_sphericity_bonded4.27536593
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 181 -
Rwork0.226 3198 -
obs-6075 100 %

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