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- PDB-8qok: Capra hircus reactive intermediate deaminase A mutant - E124A -

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Basic information

Entry
Database: PDB / ID: 8qok
TitleCapra hircus reactive intermediate deaminase A mutant - E124A
Components2-iminobutanoate/2-iminopropanoate deaminase
KeywordsUNKNOWN FUNCTION / Enzyme / deaminase
Function / homology
Function and homology information


2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds / negative regulation of translation ...2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds / negative regulation of translation / mitochondrial matrix / mRNA binding / nucleus / 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
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRizzi, G. / Visentin, C. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: Protein Sci. / Year: 2024
Title: Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus.
Authors: Rizzi, G. / Digiovanni, S. / Degani, G. / Barbiroli, A. / Di Pisa, F. / Popolo, L. / Visentin, C. / Vanoni, M.A. / Ricagno, S.
History
DepositionSep 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-iminobutanoate/2-iminopropanoate deaminase
B: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)29,0672
Polymers29,0672
Non-polymers00
Water4,324240
1
A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)87,2026
Polymers87,2026
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation4_444x-1/2,-y-1/2,-z-11
crystal symmetry operation8_444-z-1,x-1/2,-y-1/21
crystal symmetry operation12_444-y-1/2,-z-1,x-1/21
Buried area16240 Å2
ΔGint-101 kcal/mol
Surface area28970 Å2
Unit cell
Length a, b, c (Å)88.461, 88.461, 88.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-309-

HOH

31A-327-

HOH

41A-328-

HOH

51A-330-

HOH

61B-236-

HOH

71B-290-

HOH

81B-300-

HOH

91B-308-

HOH

101B-309-

HOH

111B-310-

HOH

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Components

#1: Protein 2-iminobutanoate/2-iminopropanoate deaminase


Mass: 14533.599 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capra hircus (goat) / Gene: RIDA / Production host: Escherichia coli (E. coli) / References: UniProt: P80601
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris propane 7.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.2→39.56 Å / Num. obs: 72054 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.037 / Net I/σ(I): 13.1
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.388 / Num. unique obs: 3534 / CC1/2: 0.703 / Rrim(I) all: 0.549

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.56 Å / SU ML: 0.1058 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1891 3634 5.04 %
Rwork0.1547 68402 -
obs0.1563 72036 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.08 Å2
Refinement stepCycle: LAST / Resolution: 1.2→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 240 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122108
X-RAY DIFFRACTIONf_angle_d1.19832898
X-RAY DIFFRACTIONf_chiral_restr0.0893348
X-RAY DIFFRACTIONf_plane_restr0.0134382
X-RAY DIFFRACTIONf_dihedral_angle_d5.8051322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.24121460.20962620X-RAY DIFFRACTION99.93
1.22-1.230.26261270.21442587X-RAY DIFFRACTION99.96
1.23-1.250.23441430.19572618X-RAY DIFFRACTION99.96
1.25-1.270.21211430.17722580X-RAY DIFFRACTION100
1.27-1.290.19791450.17982635X-RAY DIFFRACTION100
1.29-1.310.2181650.1822546X-RAY DIFFRACTION99.96
1.31-1.330.21531600.16732618X-RAY DIFFRACTION100
1.33-1.360.19341350.16032624X-RAY DIFFRACTION100
1.36-1.380.20161700.15252584X-RAY DIFFRACTION100
1.38-1.410.21931220.14622587X-RAY DIFFRACTION100
1.41-1.440.21041120.14462667X-RAY DIFFRACTION100
1.44-1.470.17141180.13912653X-RAY DIFFRACTION100
1.48-1.510.18431430.12812603X-RAY DIFFRACTION100
1.51-1.550.16781500.12822609X-RAY DIFFRACTION100
1.55-1.60.16131360.13322615X-RAY DIFFRACTION100
1.6-1.650.17161280.13852640X-RAY DIFFRACTION100
1.65-1.710.18611290.14552635X-RAY DIFFRACTION100
1.71-1.780.17351430.15032631X-RAY DIFFRACTION100
1.78-1.860.1821010.14542659X-RAY DIFFRACTION100
1.86-1.960.18671550.14992643X-RAY DIFFRACTION99.96
1.96-2.080.18081650.14382603X-RAY DIFFRACTION100
2.08-2.240.17311580.15012631X-RAY DIFFRACTION99.93
2.24-2.460.19621500.15222643X-RAY DIFFRACTION99.86
2.46-2.820.16721370.1642672X-RAY DIFFRACTION100
2.82-3.550.20611420.16372692X-RAY DIFFRACTION100
3.56-39.560.18361110.15292807X-RAY DIFFRACTION99.59

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