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- PDB-8qom: Capra hircus reactive intermediate deaminase A mutant - R107W -

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Basic information

Entry
Database: PDB / ID: 8qom
TitleCapra hircus reactive intermediate deaminase A mutant - R107W
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: 1.654 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

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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)29,2412
Polymers29,2412
Non-polymers00
Water2,612145
1
A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)43,8623
Polymers43,8623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
2
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)43,8623
Polymers43,8623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Unit cell
Length a, b, c (Å)88.442, 88.442, 88.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

21A-226-

HOH

31A-275-

HOH

41A-281-

HOH

51A-282-

HOH

61B-201-

HOH

71B-220-

HOH

81B-256-

HOH

91B-260-

HOH

101B-261-

HOH

111B-262-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 132 / Label seq-ID: 4 - 135

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 14620.651 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M SPG, 25% w/v PEG 1500

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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: 1.65→44.26 Å / Num. obs: 44033 / % possible obs: 99.8 % / Redundancy: 41.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.134 / Net I/σ(I): 17.9
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 1231 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.654→44.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.171 / SU B: 3.719 / SU ML: 0.062 / Average fsc free: 0.9731 / Average fsc work: 0.9813 / Cross valid method: NONE / ESU R: 0.098 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1917 1451 5.232 %
Rwork0.1645 26281 -
all0.166 --
obs-27732 99.741 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.366 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.654→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 145 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122080
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162032
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.7792854
X-RAY DIFFRACTIONr_angle_other_deg0.4321.7244682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.82758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.20110333
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.3971078
X-RAY DIFFRACTIONr_chiral_restr0.0580.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined0.2140.2347
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21651
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21052
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.214
X-RAY DIFFRACTIONr_nbd_other0.1570.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.228
X-RAY DIFFRACTIONr_mcbond_it2.3771.7821098
X-RAY DIFFRACTIONr_mcbond_other2.3251.7811098
X-RAY DIFFRACTIONr_mcangle_it3.4713.1971375
X-RAY DIFFRACTIONr_mcangle_other3.4743.1981376
X-RAY DIFFRACTIONr_scbond_it3.7822.2982
X-RAY DIFFRACTIONr_scbond_other3.782.201983
X-RAY DIFFRACTIONr_scangle_it5.3593.8431467
X-RAY DIFFRACTIONr_scangle_other5.3583.8441468
X-RAY DIFFRACTIONr_lrange_it6.73820.4852239
X-RAY DIFFRACTIONr_lrange_other6.72919.3862226
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.053757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101760.05009
12AX-RAY DIFFRACTIONLocal ncs0.101760.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.654-1.6970.274880.20918660.21220210.9650.97596.68480.18
1.697-1.7440.25710.18119260.18419980.9610.9899.950.163
1.744-1.7940.2221000.17517870.17818870.9650.981000.159
1.794-1.8490.1931070.1817910.18118980.9770.9791000.165
1.849-1.910.234940.17617200.17918140.9660.9811000.162
1.91-1.9770.258980.1816590.18417570.9570.981000.169
1.977-2.0510.179950.17116080.17117030.9820.9831000.162
2.051-2.1350.187750.16815550.16916300.9760.9831000.161
2.135-2.2290.192610.17415200.17515810.9790.9811000.169
2.229-2.3380.247720.15914180.16314900.9640.9851000.158
2.338-2.4640.181040.16413450.16514490.9790.9841000.164
2.464-2.6130.216760.17112820.17313580.970.9821000.174
2.613-2.7930.202620.16412120.16612740.9750.9831000.17
2.793-3.0150.195470.16111490.16211960.9770.9841000.169
3.015-3.3020.189580.18210490.18211070.9760.981000.196
3.302-3.6890.187620.1659470.16710090.9830.9741000.179
3.689-4.2550.164780.1418170.1438950.9840.9871000.163
4.255-5.1990.129420.1287270.1287700.9910.99199.87010.156
5.199-7.3020.225400.1755580.1795980.9720.9831000.203
7.302-44.260.179210.1653450.1663670.9850.98199.72750.204
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)
11.542-0.05770.13981.1847-0.32061.0634-0.06270.09260.0299-0.07490.09510.1739-0.0057-0.1366-0.03240.0114-0.0061-0.01340.02910.01470.0267-21.710514.981848.3562
21.1061-0.2677-0.81941.02060.48481.46660.1420.16040.0982-0.1792-0.09480.1008-0.2756-0.1838-0.04720.06890.0461-0.01010.04010.0010.029410.3931-7.754320.0234
Refinement TLS groupSelection: ALL

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