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- PDB-5n62: Human TTR crystals soaked in manganese chloride. -

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Basic information

Entry
Database: PDB / ID: 5n62
TitleHuman TTR crystals soaked in manganese chloride.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Manganese complex / metal binding / Alzheimer beta-amyloid scavenging
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7754
Polymers25,6652
Non-polymers1102
Water4,558253
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5498
Polymers51,3304
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6660 Å2
ΔGint-56 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.270, 85.830, 63.900
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
11B-409-

HOH

21B-419-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12832.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
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: 26% polyethylene glycol 4,000 (PEG4K), 0.16 M imidazole malate, pH 6.0 cryosoak: 40 % CM7 (12.5 ...Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 26% polyethylene glycol 4,000 (PEG4K), 0.16 M imidazole malate, pH 6.0 cryosoak: 40 % CM7 (12.5 % di-ethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 1,2-propanediol + 12.5 % DMSO), 25 % MPEG 5K, 5 mM MnCl2, 10 min 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: 1.891993 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.891993 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 42596 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.37 % / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rsym value: 0.163 / Net I/σ(I): 11.53
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.61 % / Rmerge(I) obs: 2.175 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 3134 / CC1/2: 0.39 / Rsym value: 2.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1J

5k1j


Resolution: 1.8→38.638 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.2445 2132 5.01 %
Rwork0.1951 --
obs0.1976 42583 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→38.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 2 253 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091933
X-RAY DIFFRACTIONf_angle_d1.0252655
X-RAY DIFFRACTIONf_dihedral_angle_d19.1131154
X-RAY DIFFRACTIONf_chiral_restr0.068297
X-RAY DIFFRACTIONf_plane_restr0.007349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84190.33221440.28392658X-RAY DIFFRACTION100
1.8419-1.8880.34341480.27662724X-RAY DIFFRACTION100
1.888-1.9390.31591410.26492697X-RAY DIFFRACTION100
1.939-1.99610.29771390.2672707X-RAY DIFFRACTION100
1.9961-2.06050.3321420.28112700X-RAY DIFFRACTION100
2.0605-2.13410.36621410.29232674X-RAY DIFFRACTION100
2.1341-2.21960.37361360.31592708X-RAY DIFFRACTION100
2.2196-2.32060.35591440.30912694X-RAY DIFFRACTION100
2.3206-2.44290.29441430.27132704X-RAY DIFFRACTION100
2.4429-2.59590.27591420.21172697X-RAY DIFFRACTION100
2.5959-2.79630.19831420.1662687X-RAY DIFFRACTION100
2.7963-3.07760.19151460.13972717X-RAY DIFFRACTION100
3.0776-3.52270.19281400.13022683X-RAY DIFFRACTION100
3.5227-4.43720.17611420.12932708X-RAY DIFFRACTION100
4.4372-38.64660.19431420.1572693X-RAY DIFFRACTION100

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