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- PDB-3u2j: Neutron crystal structure of human Transthyretin -

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Basic information

Entry
Database: PDB / ID: 3u2j
TitleNeutron crystal structure of human Transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transporter / Thyroxine Binding
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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
DEUTERATED WATER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYokoyama, T. / Mizuguchi, M. / Nabeshima, Y. / Kusaka, K. / Yamada, T. / Hosoya, T. / Ohhara, T. / Kurihara, K. / Tomoyori, K. / Tanaka, I. / Niimura, N.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin
Authors: Yokoyama, T. / Mizuguchi, M. / Nabeshima, Y. / Kusaka, K. / Yamada, T. / Hosoya, T. / Ohhara, T. / Kurihara, K. / Tomoyori, K. / Tanaka, I. / Niimura, N.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Other
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations
Category: diffrn_radiation / diffrn_source / pdbx_struct_special_symmetry
Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)25,7852
Polymers25,7852
Non-polymers00
Water99155
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)51,5704
Polymers51,5704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6300 Å2
ΔGint-48 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.094, 86.103, 66.313
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-149-

DOD

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12892.449 Da / Num. of mol.: 2 / Fragment: UNP residues 32-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M-15 / References: UniProt: P02766
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.85M tri-ammonium citrate, pD7.4, 0.4M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 3.2 - 6.2
DetectorType: wavelength-shift-fiber type of position-sensitive detector
Detector: STORAGE PHOSPHORS / Date: Nov 20, 2010
RadiationMonochromator: disk chopper / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
13.21
26.21
ReflectionResolution: 2→12.1 Å / Num. all: 15307 / Num. obs: 15307 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 11.04 Å2 / Rsym value: 0.191 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.306 / % possible all: 72.5

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Processing

Software
NameVersionClassification
iBIX_GUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
STARGazerdata reduction
STARGazerdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U2I

3u2i


Resolution: 2→12.1 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8327 / SU ML: 0.58 / σ(F): 0 / σ(I): 0 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 776 5.06 %RANDOM
Rwork0.2321 ---
obs0.234 15295 89.83 %-
all-15295 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.821 Å2 / ksol: 0.488 e/Å3
Displacement parametersBiso max: 79.22 Å2 / Biso mean: 24.2523 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.6714 Å20 Å20 Å2
2--1.4016 Å2-0 Å2
3---0.2698 Å2
Refinement stepCycle: LAST / Resolution: 2→12.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 55 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0043904
NEUTRON DIFFRACTIONf_angle_d1.4017004
NEUTRON DIFFRACTIONf_chiral_restr0.096282
NEUTRON DIFFRACTIONf_plane_restr0.004768
NEUTRON DIFFRACTIONf_dihedral_angle_d16.6751089
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0056-2.13070.34451150.33522139225480
2.1307-2.29430.30421560.28352338249487
2.2943-2.52340.31771140.25412467258190
2.5234-2.88470.25511450.23242602274795
2.8847-3.620.25891330.19962726285998
3.62-12.56020.21881300.18052595272589

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