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- PDB-5k1j: Human TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative -

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Basic information

Entry
Database: PDB / ID: 5k1j
TitleHuman TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Large conformational change / Human TTR / potentiality for scavenging beta-Amyloid in Alzheimer disease
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 / IMIDAZOLE / RHENIUM / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsStura, E.A. / Ciccone, L. / Shepard, W.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Human TTR conformation altered by rhenium tris-carbonyl derivatives.
Authors: Ciccone, L. / Policar, C. / Stura, E.A. / Shepard, W.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_special_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,36813
Polymers25,4062
Non-polymers96111
Water3,009167
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,73526
Polymers50,8134
Non-polymers1,92222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area10080 Å2
ΔGint-39 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 83.100, 65.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-384-

HOH

31A-385-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12703.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766

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Non-polymers , 6 types, 178 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Re
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 cryosoak: 40% SM2 (12.5 ...Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 cryosoak: 40% SM2 (12.5 % ethylene glycol, 12.5 % glycerol, 12.5 % 1,2-propanediol, 25 % DMSO and 37.5% 1,4-dioxane) 50% PEG 8K and 0.2 milli-M of rhenium tris-carbonyl Pyta-C8 derivative.
Temp details: temperature controlled room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryonozzle
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.175919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.175919 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 49863 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.45 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rsym value: 0.028 / Net I/σ(I): 22.92
Reflection shellResolution: 1.69→1.74 Å / Redundancy: 2.88 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.22 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PME

4pme


Resolution: 1.69→41.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.267 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22199 1332 5 %RANDOM
Rwork0.17134 ---
obs0.17391 25309 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.101 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å2-0 Å2
2---0.14 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.69→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 39 167 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192009
X-RAY DIFFRACTIONr_bond_other_d0.0020.021847
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9572749
X-RAY DIFFRACTIONr_angle_other_deg1.05734281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31524.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68615308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.511158
X-RAY DIFFRACTIONr_chiral_restr0.150.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212319
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
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_it3.2022.5061007
X-RAY DIFFRACTIONr_mcbond_other3.1692.4931003
X-RAY DIFFRACTIONr_mcangle_it4.5783.7071276
X-RAY DIFFRACTIONr_mcangle_other4.5773.7151277
X-RAY DIFFRACTIONr_scbond_it4.9573.2011002
X-RAY DIFFRACTIONr_scbond_other4.9553.2031003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5894.5421474
X-RAY DIFFRACTIONr_long_range_B_refined10.62522.8982152
X-RAY DIFFRACTIONr_long_range_B_other10.62322.9122153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.692→1.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 93 -
Rwork0.351 1780 -
obs--95.08 %

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