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- PDB-6tcd: Crystal structure of Salmo salar RidA-2 -

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Basic information

Entry
Database: PDB / ID: 6tcd
TitleCrystal structure of Salmo salar RidA-2
ComponentsRibonuclease UK114
KeywordsUNKNOWN FUNCTION / RidA / Imine Deaminase / YigF/YER057c/UK114
Function / homology2-iminobutanoate/2-iminopropanoate deaminase / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / mitochondrion / cytosol / ACETATE ION / Ribonuclease UK114
Function and homology information
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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
B: Ribonuclease UK114
C: Ribonuclease UK114
D: Ribonuclease UK114
E: Ribonuclease UK114
F: Ribonuclease UK114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,00916
Polymers88,3076
Non-polymers70110
Water14,574809
1
A: Ribonuclease UK114
B: Ribonuclease UK114
C: Ribonuclease UK114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3907
Polymers44,1543
Non-polymers2364
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-44 kcal/mol
Surface area14610 Å2
MethodPISA
2
D: Ribonuclease UK114
E: Ribonuclease UK114
F: Ribonuclease UK114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6199
Polymers44,1543
Non-polymers4656
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-104 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.883, 146.573, 53.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

21B-726-

HOH

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Components

#1: Protein
Ribonuclease UK114


Mass: 14717.908 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: UK114 / Production host: Escherichia coli (E. coli) / References: UniProt: C0H8I4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.5, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.36→83.1 Å / Num. obs: 114968 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 1 / Net I/σ(I): 16.5
Reflection shellResolution: 1.36→1.47 Å / Num. unique obs: 5748 / CC1/2: 0.628

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Processing

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

1oni


Resolution: 1.36→43.97 Å / SU ML: 0.1248 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0369
RfactorNum. reflection% reflection
Rfree0.1837 5624 4.89 %
Rwork0.1594 --
obs0.1606 114898 66.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.36→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 27 809 6649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00595965
X-RAY DIFFRACTIONf_angle_d0.79968113
X-RAY DIFFRACTIONf_chiral_restr0.0706950
X-RAY DIFFRACTIONf_plane_restr0.0041061
X-RAY DIFFRACTIONf_dihedral_angle_d19.58222148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.370.18920.274777X-RAY DIFFRACTION1.4
1.37-1.390.2938200.2564300X-RAY DIFFRACTION5.66
1.39-1.410.2774280.2531489X-RAY DIFFRACTION9.15
1.41-1.420.3152350.2264711X-RAY DIFFRACTION13.24
1.42-1.440.2624630.22681160X-RAY DIFFRACTION21.52
1.44-1.460.2337920.22581627X-RAY DIFFRACTION30.41
1.46-1.480.28481100.21332019X-RAY DIFFRACTION37.4
1.48-1.510.23861350.1962280X-RAY DIFFRACTION43.01
1.51-1.530.23961300.18652578X-RAY DIFFRACTION47.59
1.53-1.560.22941210.18862813X-RAY DIFFRACTION52.03
1.56-1.580.21411240.18952994X-RAY DIFFRACTION54.74
1.58-1.610.21051600.18293175X-RAY DIFFRACTION58.84
1.61-1.640.24621620.18723323X-RAY DIFFRACTION61.62
1.64-1.680.21181770.18443542X-RAY DIFFRACTION64.88
1.68-1.710.22822050.18323766X-RAY DIFFRACTION69.86
1.71-1.750.1872110.19044012X-RAY DIFFRACTION74.41
1.75-1.80.22131950.1794291X-RAY DIFFRACTION78.5
1.8-1.840.24072280.1684677X-RAY DIFFRACTION85.95
1.84-1.90.20772840.16294943X-RAY DIFFRACTION91.86
1.9-1.960.19872670.15755339X-RAY DIFFRACTION98.37
1.96-2.030.1932920.15235411X-RAY DIFFRACTION100
2.03-2.110.17962910.14375472X-RAY DIFFRACTION100
2.11-2.210.1772510.15155471X-RAY DIFFRACTION99.98
2.21-2.320.1592650.14385491X-RAY DIFFRACTION99.98
2.32-2.470.1722630.16035492X-RAY DIFFRACTION100
2.47-2.660.19333010.16785474X-RAY DIFFRACTION100
2.66-2.930.19693150.17245474X-RAY DIFFRACTION99.98
2.93-3.350.17322850.16625551X-RAY DIFFRACTION99.98
3.35-4.220.17223110.14495572X-RAY DIFFRACTION100
4.22-43.970.15043010.1445750X-RAY DIFFRACTION98.9

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