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- PDB-7kjj: Reconstructed ancestor of HIUases and Transthyretins -

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Basic information

Entry
Database: PDB / ID: 7kjj
TitleReconstructed ancestor of HIUases and Transthyretins
ComponentsTTR ancestor
KeywordsTRANSPORT PROTEIN / HORMONE TRANSPORT
Function / homology3,5,3',5'-TETRAIODO-L-THYRONINE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsNagem, R.A.P. / Bleicher, L. / Costa, M.A.F.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel23038.010059/2013-15 AUXPE 3379/2013 Brazil
CitationJournal: J.Mol.Evol. / Year: 2021
Title: Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies.
Authors: Carrijo de Oliveira, L. / Figueiredo Costa, M.A. / Goncalves Pedersolli, N. / Heleno Batista, F.A. / Migliorini Figueira, A.C. / Salgado Ferreira, R. / Alves Pinto Nagem, R. / Alves Nahum, L. / Bleicher, L.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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: TTR ancestor
B: TTR ancestor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5885
Polymers28,9722
Non-polymers1,6163
Water3,207178
1
A: TTR ancestor
B: TTR ancestor
hetero molecules

A: TTR ancestor
B: TTR ancestor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,17610
Polymers57,9444
Non-polymers3,2326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10130 Å2
ΔGint-27 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.430, 92.430, 87.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21B-334-

HOH

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Components

#1: Protein TTR ancestor


Mass: 14486.085 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TTR ancestor is a reconstruction of the node right after duplication, corresponding to the ancestor of all modern transthyretins
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Condition 1: 2 M lithium sulfate, 5% (v/v) 2-propanol, 0.1 M magnesium sulfate, 0.2 M sodium acetate pH 4.5 Condition 2: 30% (w/v) PEG 1500, 20% (w/v) PEG 400, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.55→41.34 Å / Num. obs: 55503 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.037 / Net I/σ(I): 26.3
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7752 / CC1/2: 0.868 / Rrim(I) all: 0.703 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Cootmodel building
PHENIX1.14_3260phasing
PHENIX1.14_3260refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→40.89 Å / SU ML: 0.1069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8035 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1846 2666 4.81 %
Rwork0.1721 52811 -
obs0.1727 55477 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.24 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 52 178 2022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01571915
X-RAY DIFFRACTIONf_angle_d1.47462622
X-RAY DIFFRACTIONf_chiral_restr0.0991299
X-RAY DIFFRACTIONf_plane_restr0.0103324
X-RAY DIFFRACTIONf_dihedral_angle_d16.5707650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.23441460.20992701X-RAY DIFFRACTION99.3
1.58-1.610.22911290.20092753X-RAY DIFFRACTION99.97
1.61-1.640.20271400.17062738X-RAY DIFFRACTION99.93
1.64-1.680.19361390.16462749X-RAY DIFFRACTION99.97
1.68-1.720.19761410.16252726X-RAY DIFFRACTION99.97
1.72-1.760.16941390.16712736X-RAY DIFFRACTION100
1.76-1.810.1931350.1592754X-RAY DIFFRACTION99.97
1.81-1.860.17471200.15372767X-RAY DIFFRACTION100
1.86-1.920.18831250.1452786X-RAY DIFFRACTION100
1.92-1.990.14671360.14762762X-RAY DIFFRACTION100
1.99-2.070.14031360.14682764X-RAY DIFFRACTION100
2.07-2.160.18231340.15532764X-RAY DIFFRACTION100
2.16-2.280.16841330.16112796X-RAY DIFFRACTION99.97
2.28-2.420.18511540.16942770X-RAY DIFFRACTION100
2.42-2.610.18951560.18372789X-RAY DIFFRACTION100
2.61-2.870.20961390.1762796X-RAY DIFFRACTION100
2.87-3.280.21371730.18832808X-RAY DIFFRACTION99.93
3.28-4.140.15751470.16272853X-RAY DIFFRACTION99.93
4.14-40.890.19021440.18932999X-RAY DIFFRACTION99.12

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