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- PDB-5n5q: Human TTR altered conformation from soaking in iron chloride. -

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Basic information

Entry
Database: PDB / ID: 5n5q
TitleHuman TTR altered conformation from soaking in iron chloride.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Conformational change / Iron clusters / metal binding protein / Alzheimer beta-amyloid scavenging
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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, 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 / : / Chem-FFE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsCiccone, L. / Savko, M. / Shepard, W. / Stura, E.A.
CitationJournal: Sci Rep / Year: 2018
Title: Copper mediated amyloid-beta binding to Transthyretin.
Authors: Ciccone, L. / Fruchart-Gaillard, C. / Mourier, G. / Savko, M. / Nencetti, S. / Orlandini, E. / Servent, D. / Stura, E.A. / Shepard, W.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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_symmetry

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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)26,24911
Polymers25,4062
Non-polymers8439
Water1,820101
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,49922
Polymers50,8134
Non-polymers1,68618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area7920 Å2
ΔGint-128 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.730, 81.810, 69.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FFE / [bis(oxidanyl)-[tetrakis(oxidanyl)ferriooxy]ferrio]oxy-pentakis(oxidanyl)iron


Mass: 386.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3H11O13
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
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: 27 % polyethylene glycol 4,000, 0.2 M imidazole malate, pH 6.0. cryosoak: 40% SM3 (, 25 % MPEG ...Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 27 % polyethylene glycol 4,000, 0.2 M imidazole malate, pH 6.0. cryosoak: 40% SM3 (, 25 % MPEG 5K, 25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 25 % MPEG 5K, 0.1 M CHC (citric acid, HEPES, CHES: 90 % acid /10 % basic), 30 mM FeCl2, 2 h soak.
PH range: 6 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.73915 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73915 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 15593 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.21 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rsym value: 0.185 / Net I/σ(I): 8.28
Reflection shellResolution: 2.53→2.68 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 2460 / CC1/2: 0.3 / Rsym value: 1.82 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1J

5k1j


Resolution: 2.53→40.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.111 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.416 / ESU R Free: 0.321 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25252 427 5 %RANDOM
Rwork0.19205 ---
obs0.19508 8113 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.976 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å20 Å2
2--1.74 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.53→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 33 101 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191918
X-RAY DIFFRACTIONr_bond_other_d0.0020.021725
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9672624
X-RAY DIFFRACTIONr_angle_other_deg0.93233987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47323.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.591159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02391
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_it3.8524.953955
X-RAY DIFFRACTIONr_mcbond_other3.8514.938950
X-RAY DIFFRACTIONr_mcangle_it6.2687.3931194
X-RAY DIFFRACTIONr_mcangle_other6.2667.3981195
X-RAY DIFFRACTIONr_scbond_it5.6575.841963
X-RAY DIFFRACTIONr_scbond_other5.6545.845964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5598.4891431
X-RAY DIFFRACTIONr_long_range_B_refined12.22358.8591962
X-RAY DIFFRACTIONr_long_range_B_other12.24858.7651952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.531→2.597 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 28 -
Rwork0.41 548 -
obs--92.9 %

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