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- PDB-7zs6: Crystal structure of Apis mellifera RidA -

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Basic information

Entry
Database: PDB / ID: 7zs6
TitleCrystal structure of Apis mellifera RidA
ComponentsReactive intermediate deaminase A
KeywordsUNKNOWN FUNCTION / Deiminase / Ractive intermediate deaminase
Function / homology
Function and homology information


deaminase activity / 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
2-iminobutanoate/2-iminopropanoate deaminase isoform X1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsVisentin, C. / Rizzi, G. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Apis mellifera RidA, a novel member of the canonical YigF/YER057c/UK114 imine deiminase superfamily of enzymes pre-empting metabolic damage.
Authors: Visentin, C. / Rizzi, G. / Degani, G. / Digiovanni, S. / Robecchi, G. / Barbiroli, A. / Popolo, L. / Vanoni, M.A. / Ricagno, S.
History
DepositionMay 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Reactive intermediate deaminase A
BBB: Reactive intermediate deaminase A
CCC: Reactive intermediate deaminase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3396
Polymers46,2293
Non-polymers1093
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-46 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.499, 109.499, 141.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11BBB-502-

MG

21AAA-333-

HOH

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Components

#1: Protein Reactive intermediate deaminase A


Mass: 15409.731 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7M7GBQ0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M MES, 20% PEG 6000 pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.31→43.305 Å / Num. obs: 101696 / % possible obs: 99.44 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.8
Reflection shellResolution: 1.31→1.33 Å / Rmerge(I) obs: 1.236 / Num. unique obs: 4890 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONI

1oni


Resolution: 1.31→43.305 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.98 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1644 5097 5.012 %
Rwork0.1305 96599 -
all0.132 --
obs-101696 99.381 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.032 Å2-0 Å2-0 Å2
2--0.032 Å20 Å2
3----0.065 Å2
Refinement stepCycle: LAST / Resolution: 1.31→43.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 6 420 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133699
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173785
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.6435141
X-RAY DIFFRACTIONr_angle_other_deg1.4851.5748829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16725.298168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40515725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6131510
X-RAY DIFFRACTIONr_chiral_restr0.1150.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024344
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02792
X-RAY DIFFRACTIONr_nbd_refined0.2390.2731
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23661
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21802
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.217
X-RAY DIFFRACTIONr_nbd_other0.2340.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.218
X-RAY DIFFRACTIONr_mcbond_it2.7782.0871794
X-RAY DIFFRACTIONr_mcbond_other2.7482.0841793
X-RAY DIFFRACTIONr_mcangle_it3.0473.1342291
X-RAY DIFFRACTIONr_mcangle_other3.0513.1362292
X-RAY DIFFRACTIONr_scbond_it4.6292.5781904
X-RAY DIFFRACTIONr_scbond_other4.6292.5781904
X-RAY DIFFRACTIONr_scangle_it5.0583.6852782
X-RAY DIFFRACTIONr_scangle_other5.0553.6842782
X-RAY DIFFRACTIONr_lrange_it4.57926.5384254
X-RAY DIFFRACTIONr_lrange_other4.47925.9064156
X-RAY DIFFRACTIONr_rigid_bond_restr4.32337481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.3440.3223580.3037001X-RAY DIFFRACTION98.3035
1.344-1.380.3033470.2776886X-RAY DIFFRACTION99.45
1.38-1.420.2753540.2436737X-RAY DIFFRACTION99.4949
1.42-1.4640.2322940.2026573X-RAY DIFFRACTION99.5506
1.464-1.5120.2013290.176275X-RAY DIFFRACTION98.8771
1.512-1.5650.2113050.146176X-RAY DIFFRACTION99.5392
1.565-1.6240.1692930.1145926X-RAY DIFFRACTION99.5837
1.624-1.690.1613120.1095707X-RAY DIFFRACTION99.7018
1.69-1.7660.1552910.15483X-RAY DIFFRACTION99.7754
1.766-1.8520.1652900.0995239X-RAY DIFFRACTION99.7654
1.852-1.9520.1472640.1024977X-RAY DIFFRACTION99.6009
1.952-2.070.1462500.1054772X-RAY DIFFRACTION99.8807
2.07-2.2130.1412500.1034449X-RAY DIFFRACTION99.9149
2.213-2.390.1322370.1014166X-RAY DIFFRACTION99.9319
2.39-2.6180.1592060.1043865X-RAY DIFFRACTION99.755
2.618-2.9270.1572090.1153451X-RAY DIFFRACTION99.2408
2.927-3.3790.1751650.1343094X-RAY DIFFRACTION99.3901
3.379-4.1370.1561490.1272604X-RAY DIFFRACTION98.6385

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