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- PDB-8qov: Capra hircus reactive intermediate deaminase A mutant - I126Y -

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Basic information

Entry
Database: PDB / ID: 8qov
TitleCapra hircus reactive intermediate deaminase A mutant - I126Y
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 / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / 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 / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / 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
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / 2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRizzi, G. / Visentin, C. / Di Pisa, F. / 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 / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5105
Polymers29,2832
Non-polymers2273
Water2,666148
1
A: 2-iminobutanoate/2-iminopropanoate deaminase
B: 2-iminobutanoate/2-iminopropanoate deaminase
hetero molecules

A: 2-iminobutanoate/2-iminopropanoate deaminase
B: 2-iminobutanoate/2-iminopropanoate deaminase
hetero molecules

A: 2-iminobutanoate/2-iminopropanoate deaminase
B: 2-iminobutanoate/2-iminopropanoate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,53115
Polymers87,8506
Non-polymers6819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area18490 Å2
ΔGint-109 kcal/mol
Surface area28380 Å2
Unit cell
Length a, b, c (Å)88.746, 88.746, 88.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

21A-678-

HOH

31A-679-

HOH

41B-307-

HOH

51B-335-

HOH

61B-361-

HOH

71B-362-

HOH

81B-369-

HOH

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Components

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


Mass: 14641.651 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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 38.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M MgCl hexahydrate, 0.1 M HEPES, 22% w/v poly(acrylic acid sodium salt)5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 31, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.6→39.69 Å / Num. obs: 31014 / % possible obs: 100 % / Redundancy: 41.3 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.07 / Net I/σ(I): 31.2
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1523 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.547 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21621 1459 4.7 %RANDOM
Rwork0.18951 ---
obs0.19082 29491 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.982 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 12 148 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122064
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162022
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6332812
X-RAY DIFFRACTIONr_angle_other_deg0.561.5574651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.066510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1210326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8862.3531094
X-RAY DIFFRACTIONr_mcbond_other1.8862.3521094
X-RAY DIFFRACTIONr_mcangle_it2.6114.2261367
X-RAY DIFFRACTIONr_mcangle_other2.6124.2261368
X-RAY DIFFRACTIONr_scbond_it2.8612.656970
X-RAY DIFFRACTIONr_scbond_other2.8622.657971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1794.7271440
X-RAY DIFFRACTIONr_long_range_B_refined5.48727.282257
X-RAY DIFFRACTIONr_long_range_B_other5.47526.52236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 64 -
Rwork0.291 2194 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6555-0.2498-0.57660.58880.68680.9992-0.1672-0.2597-0.078-0.01790.14710.03990.05690.31260.02010.0540.04870.02750.13-0.00150.063-30.068132.30671.675
20.4558-0.08440.45630.5371-0.14730.47430.1253-0.0219-0.07230.0502-0.0529-0.02520.1043-0.0164-0.07240.06480.0025-0.0240.0358-0.00340.0282-7.04770.6265-26.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 501
2X-RAY DIFFRACTION2B1 - 201

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