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- PDB-8q3h: Capra hircus reactive intermediate deaminase A mutant - A108D -

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Basic information

Entry
Database: PDB / ID: 8q3h
TitleCapra hircus reactive intermediate deaminase A mutant - A108D
Components2-iminobutanoate/2-iminopropanoate deaminase
KeywordsUNKNOWN FUNCTION / 2-iminobutanoate/2-iminopropanoate deaminase - Capra hircus
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: 1.57 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
DepositionAug 4, 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)29,4254
Polymers29,2712
Non-polymers1542
Water3,963220
1
A: 2-iminobutanoate/2-iminopropanoate deaminase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)44,3699
Polymers43,9073
Non-polymers4626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8110 Å2
ΔGint-31 kcal/mol
Surface area15600 Å2
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)43,9073
Polymers43,9073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7370 Å2
ΔGint-35 kcal/mol
Surface area15410 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
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-309-

HOH

21A-341-

HOH

31A-406-

HOH

41A-424-

HOH

51A-425-

HOH

61B-224-

HOH

71B-274-

HOH

81B-286-

HOH

91B-287-

HOH

101B-288-

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: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 135 / Label seq-ID: 4 - 138

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: 14635.646 Da / Num. of mol.: 2 / Mutation: A108D
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-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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / 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: 1.57→44.27 Å / Num. obs: 62170 / % possible obs: 100 % / Redundancy: 41.2 % / Biso Wilson estimate: 19.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.05 / Net I/σ(I): 41.08
Reflection shellResolution: 1.57→1.67 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 10.78 / Num. unique obs: 1526 / CC1/2: 0.99 / Rrim(I) all: 0.0267

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→44.27 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.15 / SU B: 3.325 / SU ML: 0.054 / Average fsc free: 0.9766 / Average fsc work: 0.9873 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1786 1563 4.834 %
Rwork0.1424 30771 -
all0.144 --
obs-32334 99.636 %
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: 25.116 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.57→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 10 220 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122098
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162080
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.7862873
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7254795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.456510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07210343
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3911078
X-RAY DIFFRACTIONr_chiral_restr0.0890.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2110.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21793
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21053
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.215
X-RAY DIFFRACTIONr_nbd_other0.1710.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.236
X-RAY DIFFRACTIONr_mcbond_it6.2132.5281104
X-RAY DIFFRACTIONr_mcbond_other6.1812.5291104
X-RAY DIFFRACTIONr_mcangle_it9.1554.5451383
X-RAY DIFFRACTIONr_mcangle_other9.1574.5481384
X-RAY DIFFRACTIONr_scbond_it6.7062.796994
X-RAY DIFFRACTIONr_scbond_other6.7032.799995
X-RAY DIFFRACTIONr_scangle_it10.0025.0171477
X-RAY DIFFRACTIONr_scangle_other9.9995.0191478
X-RAY DIFFRACTIONr_lrange_it15.55928.7672273
X-RAY DIFFRACTIONr_lrange_other14.40825.8452212
X-RAY DIFFRACTIONr_rigid_bond_restr4.08434178
X-RAY DIFFRACTIONr_ncsr_local_group_10.1290.053732
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.128710.05008
12AX-RAY DIFFRACTIONLocal ncs0.128710.05008
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
1.57-1.6110.2251210.15621850.1623620.9690.98597.62910.139
1.611-1.6550.2141130.15222040.15523170.9720.9861000.139
1.655-1.7030.213930.1521690.15322620.9710.9861000.138
1.703-1.7550.2031040.14220520.14521560.9730.9881000.131
1.755-1.8130.265950.13520510.1421460.960.9881000.126
1.813-1.8760.1921050.1419250.14320300.9770.9881000.132
1.876-1.9470.18920.13619110.13820030.9810.9891000.131
1.947-2.0260.193810.12918290.13219100.980.9911000.127
2.026-2.1160.157700.13617460.13718160.9840.9861000.133
2.116-2.2190.188940.13616870.13917810.9780.9891000.137
2.219-2.3390.192690.13315750.13516440.9770.9891000.136
2.339-2.4810.167840.13615240.13816080.9810.9881000.142
2.481-2.6510.201670.14214210.14514880.9760.9881000.151
2.651-2.8630.184800.1313120.13313920.9770.9891000.141
2.863-3.1350.16670.14612380.14713050.9810.9871000.159
3.135-3.5030.157640.15311030.15411680.9870.98699.91440.17
3.503-4.040.165710.1349780.13610500.9830.98999.90480.157
4.04-4.9380.151330.128540.1218920.990.99299.43950.148
4.938-6.940.168440.1516480.1526940.9860.98999.71180.185
6.94-44.270.216160.2693590.2664260.9670.93788.02820.368
Refinement TLS params.

T11: 0.0008 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0430.00570.01040.08960.02680.0543-0.0009-0.0007-0.00240.00150.00210.00270.00520.0013-0.0012-0.0001-0.00040.00040.00030.0014-4.0625-21.7461-14.8262
20.01120.00990.02380.1111-0.00640.05820.0010.00760.00150.0002-0.00120.00580.0040.01890.00020.00080.00070.0083-0.00260.004624.275210.5287.633
Refinement TLS groupSelection: ALL

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