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- PDB-5k1n: Human TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative -

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Basic information

Entry
Database: PDB / ID: 5k1n
TitleHuman TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Large conformational change / Human TTR / potentiality for scavenging beta-Amyloid in Alzheimer disease
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/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 / DI(HYDROXYETHYL)ETHER / RHENIUM / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,91811
Polymers25,9232
Non-polymers9959
Water2,774154
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,83622
Polymers51,8464
Non-polymers1,99018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area9570 Å2
ΔGint-58 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 82.130, 67.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12961.511 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 , 7 types, 163 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Re
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-IMD / IMIDAZOLE


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


Mass: 18.015 Da / Num. of mol.: 154 / 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: 46.23 %
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 + 3.6% polyethylene ...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 + 3.6% polyethylene glycol monomethyl ether (MPEG5K), 30 mM sodium acetate pH 5.5 cryosoak: 40% SM3 (25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 50% PEG 8K and 0.5 milli-M of rhenium tris-carbonyl Pyta-C12 derivative.
PH range: 5.5-6.0 / 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 9M / Detector: PIXEL / Date: Apr 22, 2016 / Details: mirrors
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.175919 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 41147 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rsym value: 0.052 / Net I/σ(I): 12.31
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.69 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1J

5k1j


Resolution: 1.81→41.065 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 24.74
RfactorNum. reflection% reflection
Rfree0.2239 2050 4.99 %
Rwork0.1888 --
obs0.1906 41116 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→41.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 31 154 1970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052056
X-RAY DIFFRACTIONf_angle_d0.8192808
X-RAY DIFFRACTIONf_dihedral_angle_d18.2691218
X-RAY DIFFRACTIONf_chiral_restr0.056305
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85220.33761370.33242639X-RAY DIFFRACTION98
1.8522-1.89850.31071380.29172559X-RAY DIFFRACTION99
1.8985-1.94980.32411410.26422642X-RAY DIFFRACTION98
1.9498-2.00720.27481340.2282607X-RAY DIFFRACTION98
2.0072-2.0720.23561310.21942552X-RAY DIFFRACTION98
2.072-2.1460.25161350.20392617X-RAY DIFFRACTION98
2.146-2.23190.25731370.20482600X-RAY DIFFRACTION98
2.2319-2.33350.24151360.2042572X-RAY DIFFRACTION97
2.3335-2.45650.26331390.19562598X-RAY DIFFRACTION98
2.4565-2.61040.20241370.18232618X-RAY DIFFRACTION99
2.6104-2.81190.23841400.16932638X-RAY DIFFRACTION99
2.8119-3.09480.22841400.1732634X-RAY DIFFRACTION99
3.0948-3.54240.19361370.15222589X-RAY DIFFRACTION98
3.5424-4.46220.16791320.14972561X-RAY DIFFRACTION97
4.4622-41.07560.22511360.20322640X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 43.2491 Å / Origin y: 28.2877 Å / Origin z: 17.264 Å
111213212223313233
T0.141 Å20.0016 Å2-0.0129 Å2-0.1502 Å2-0.0015 Å2--0.1582 Å2
L0.3094 °20.0003 °2-0.308 °2-0.6328 °20.0276 °2--0.4438 °2
S-0.0511 Å °-0.0073 Å °-0.0598 Å °0.0097 Å °0.0049 Å °-0.0254 Å °-0.0252 Å °0.0208 Å °0 Å °
Refinement TLS groupSelection details: all

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