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

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Basic information

Entry
Database: PDB / ID: 7kcn
TitleReconstructed ancestor of HIUases and Transthyretins
ComponentsHIUase-TTR ancestor
KeywordsUNKNOWN FUNCTION / probably a 5-hydroxyisourate hydrolase
Function / homologyTransthyretin/hydroxyisourate hydrolase domain / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.46 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 6, 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 1.2Aug 18, 2021Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIUase-TTR ancestor
B: HIUase-TTR ancestor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,99012
Polymers27,3372
Non-polymers65410
Water3,657203
1
A: HIUase-TTR ancestor
B: HIUase-TTR ancestor
hetero molecules

A: HIUase-TTR ancestor
B: HIUase-TTR ancestor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,98024
Polymers54,6734
Non-polymers1,30720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area9660 Å2
ΔGint-19 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.030, 67.030, 116.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21B-320-

HOH

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Components

#1: Protein HIUase-TTR ancestor


Mass: 13668.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This protein sequence was designed (reconstructed) to represent an HIUase-TTR ancestor before gene duplication
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20-24% (w/v) PEG 1,500, 20-30% (v/v) glycerol

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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 PILATUS 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: 1.46→44.05 Å / Num. obs: 45814 / % possible obs: 97.1 % / Redundancy: 11.5 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 24.7
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 11794 / CC1/2: 0.933 / Rrim(I) all: 0.353 / % possible all: 82.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
PHENIX1.14_3260phasing
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.46→30.1 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9076 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1817 2202 4.81 %
Rwork0.1613 43591 -
obs0.1623 45793 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.13 Å2
Refinement stepCycle: LAST / Resolution: 1.46→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 41 203 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01551991
X-RAY DIFFRACTIONf_angle_d1.52372718
X-RAY DIFFRACTIONf_chiral_restr0.1209304
X-RAY DIFFRACTIONf_plane_restr0.0102340
X-RAY DIFFRACTIONf_dihedral_angle_d18.0337725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.2505960.22911931X-RAY DIFFRACTION70.63
1.49-1.530.20661240.19512597X-RAY DIFFRACTION95.41
1.53-1.570.22581410.18942657X-RAY DIFFRACTION97.36
1.57-1.610.19771340.17662732X-RAY DIFFRACTION99.07
1.61-1.660.22681440.17622741X-RAY DIFFRACTION99.9
1.66-1.710.20851270.17782758X-RAY DIFFRACTION100
1.71-1.770.20971440.17072754X-RAY DIFFRACTION100
1.77-1.840.19381430.17022753X-RAY DIFFRACTION100
1.84-1.920.17531460.16852778X-RAY DIFFRACTION100
1.92-2.030.19651430.15812766X-RAY DIFFRACTION100
2.03-2.150.17521370.1572787X-RAY DIFFRACTION100
2.15-2.320.19571310.15662810X-RAY DIFFRACTION100
2.32-2.550.18411470.17012797X-RAY DIFFRACTION99.93
2.55-2.920.20171390.16222839X-RAY DIFFRACTION99.93
2.92-3.680.16131490.14452863X-RAY DIFFRACTION100
3.68-30.10.16331570.15833028X-RAY DIFFRACTION99.53

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