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- PDB-5llv: Crystal structure of DACM F87M/L110M Transthyretin mutant -

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Basic information

Entry
Database: PDB / ID: 5llv
TitleCrystal structure of DACM F87M/L110M Transthyretin mutant
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Tetramer / Protein aggregation / N-(7-Dimethylamino-4-Methylcoumarin-3-yl))Maleimide
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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, 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
Similarity search - Domain/homology
ACETATE ION / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSala, B.M. / Ghadami, S.A. / Bemporad, F. / Chiti, F. / Ricagno, S.
CitationJournal: Cell. Mol. Life Sci. / Year: 2017
Title: FRET studies of various conformational states adopted by transthyretin.
Authors: Ghadami, S.A. / Bemporad, F. / Sala, B.M. / Tiana, G. / Ricagno, S. / Chiti, F.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Structure summary / Category: audit_author
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)55,98511
Polymers55,6424
Non-polymers3437
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-87 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.441, 83.760, 86.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13910.616 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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.84 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M CaCl2 0.1 M Sodium Acetate pH 4.6 20% v/v 2-propanol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2015 / Details: KB mirro
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→22.04 Å / Num. obs: 52003 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GKO

1gko


Resolution: 1.7→22.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.697 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22308 2619 5 %RANDOM
Rwork0.14953 ---
obs0.15328 49331 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.38 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 19 182 3773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193824
X-RAY DIFFRACTIONr_bond_other_d0.0010.023548
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9495248
X-RAY DIFFRACTIONr_angle_other_deg0.80538247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3632.061908
X-RAY DIFFRACTIONr_mcbond_other4.3242.0541903
X-RAY DIFFRACTIONr_mcangle_it5.1863.0682386
X-RAY DIFFRACTIONr_mcangle_other5.1863.0712387
X-RAY DIFFRACTIONr_scbond_it6.6192.671916
X-RAY DIFFRACTIONr_scbond_other6.6182.671917
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6433.772837
X-RAY DIFFRACTIONr_long_range_B_refined8.11523.5313010
X-RAY DIFFRACTIONr_long_range_B_other8.11423.5363011
X-RAY DIFFRACTIONr_rigid_bond_restr4.12537372
X-RAY DIFFRACTIONr_sphericity_free33.845573
X-RAY DIFFRACTIONr_sphericity_bonded17.13857364
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 185 -
Rwork0.325 3614 -
obs--99.79 %

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