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- PDB-6tcc: Crystal structure of Salmo salar RidA-1 -

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Basic information

Entry
Database: PDB / ID: 6tcc
TitleCrystal structure of Salmo salar RidA-1
Componentsribonuclease UK114
KeywordsUNKNOWN FUNCTION / RidA / Imine Deaminase / YigF/YER057c/UK114
Function / homology
Function and homology information


2-iminobutanoate/2-iminopropanoate deaminase / mitochondrion / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Ribonuclease UK114
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRicagno, S. / Visentin, C. / Di Pisa, F. / Digiovanni, S. / Oberti, L. / Degani, G. / Popolo, L. / Bartorelli, A.
CitationJournal: Sci Rep / Year: 2020
Title: Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage.
Authors: Digiovanni, S. / Visentin, C. / Degani, G. / Barbiroli, A. / Chiara, M. / Regazzoni, L. / Di Pisa, F. / Borchert, A.J. / Downs, D.M. / Ricagno, S. / Vanoni, M.A. / Popolo, L.
History
DepositionNov 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ribonuclease UK114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4694
Polymers14,2411
Non-polymers2273
Water1,69394
1
A: ribonuclease UK114
hetero molecules

A: ribonuclease UK114
hetero molecules

A: ribonuclease UK114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,40612
Polymers42,7243
Non-polymers6829
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area9360 Å2
ΔGint-13 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.189, 52.189, 242.565
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-378-

HOH

31A-387-

HOH

41A-393-

HOH

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Components

#1: Protein ribonuclease UK114


Mass: 14241.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: hrsp12 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S3KNQ3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.2 M Sodium acetate pH 5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.65 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.05→42.35 Å / Num. obs: 60156 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 11.74 Å2 / CC1/2: 1 / Net I/σ(I): 21.1
Reflection shellResolution: 1.05→1.11 Å / Num. unique obs: 8683 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONI

1oni


Resolution: 1.05→33.07 Å / SU ML: 0.0753 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0811
RfactorNum. reflection% reflection
Rfree0.1633 3076 5.12 %
Rwork0.1448 --
obs0.1458 60133 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.05→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 15 94 1084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851027
X-RAY DIFFRACTIONf_angle_d1.06131397
X-RAY DIFFRACTIONf_chiral_restr0.0789168
X-RAY DIFFRACTIONf_plane_restr0.0063181
X-RAY DIFFRACTIONf_dihedral_angle_d14.1731375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.23481560.22362531X-RAY DIFFRACTION99.7
1.07-1.080.22581240.20912575X-RAY DIFFRACTION99.93
1.08-1.10.19221490.19332542X-RAY DIFFRACTION100
1.1-1.120.19651300.16912565X-RAY DIFFRACTION99.96
1.12-1.140.18031120.15922581X-RAY DIFFRACTION99.96
1.14-1.170.16941330.14712572X-RAY DIFFRACTION99.93
1.17-1.190.17291320.14722584X-RAY DIFFRACTION99.93
1.19-1.220.14171580.13782548X-RAY DIFFRACTION99.93
1.22-1.250.17311330.13842553X-RAY DIFFRACTION99.96
1.25-1.280.16691310.13742591X-RAY DIFFRACTION99.96
1.28-1.320.14531510.13192544X-RAY DIFFRACTION100
1.32-1.370.17621340.13172599X-RAY DIFFRACTION99.93
1.37-1.410.14581420.13222591X-RAY DIFFRACTION100
1.41-1.470.15551430.132544X-RAY DIFFRACTION100
1.47-1.540.1491410.12622624X-RAY DIFFRACTION100
1.54-1.620.15051390.1242571X-RAY DIFFRACTION100
1.62-1.720.14921330.13032609X-RAY DIFFRACTION100
1.72-1.850.14281670.1372585X-RAY DIFFRACTION100
1.85-2.040.18351420.13132609X-RAY DIFFRACTION100
2.04-2.330.15121500.13012646X-RAY DIFFRACTION100
2.33-2.940.17491310.14532683X-RAY DIFFRACTION100

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