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- PDB-8qoq: Capra hircus reactive intermediate deaminase A mutant - R107A -

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Basic information

Entry
Database: PDB / ID: 8qoq
TitleCapra hircus reactive intermediate deaminase A mutant - R107A
Components2-iminobutanoate/2-iminopropanoate deaminase
KeywordsUNKNOWN FUNCTION / Enzyme / deaminase
Function / homology
Function and homology information


: / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / Hydrolases; Acting on ester bonds ...: / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / 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
2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.214 Å
AuthorsRizzi, G. / Visentin, C. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: To Be Published
Title: Capra hircus reactive intermediate deaminase A mutant - R107A
Authors: Rizzi, G. / Visentin, C. / Ricagno, S.
History
DepositionSep 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)29,0112
Polymers29,0112
Non-polymers00
Water3,549197
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)87,0336
Polymers87,0336
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation3_454-x-1,y+1/2,-z-1/21
crystal symmetry operation8_454-z-1,x+1/2,-y-1/21
crystal symmetry operation10_454-y-1,z+1/2,-x-1/21
Buried area17330 Å2
ΔGint-105 kcal/mol
Surface area27600 Å2
Unit cell
Length a, b, c (Å)87.280, 87.280, 87.280
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-238-

HOH

21A-304-

HOH

31A-317-

HOH

41B-230-

HOH

51B-273-

HOH

61B-278-

HOH

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Components

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


Mass: 14505.519 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.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane 8.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.21→43.64 Å / Num. obs: 66673 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.056 / Net I/σ(I): 9.9
Reflection shellResolution: 1.21→1.24 Å / Rmerge(I) obs: 0.768 / Num. unique obs: 3196 / CC1/2: 0.189 / Rrim(I) all: 1.086

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.214→39.033 Å / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1697 3288 4.95 %
Rwork0.1463 --
obs0.1474 66448 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.214→39.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 197 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162150
X-RAY DIFFRACTIONf_angle_d1.4582958
X-RAY DIFFRACTIONf_dihedral_angle_d6.7631385
X-RAY DIFFRACTIONf_chiral_restr0.086352
X-RAY DIFFRACTIONf_plane_restr0.008389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2144-1.23260.31271090.25872478X-RAY DIFFRACTION90
1.2326-1.25180.28711290.21242733X-RAY DIFFRACTION100
1.2518-1.27240.21711400.19752791X-RAY DIFFRACTION100
1.2724-1.29430.22151300.18782716X-RAY DIFFRACTION100
1.2943-1.31780.22061360.18492718X-RAY DIFFRACTION100
1.3178-1.34320.19981690.17262739X-RAY DIFFRACTION100
1.3432-1.37060.18161310.17542746X-RAY DIFFRACTION100
1.3706-1.40040.22151650.16442715X-RAY DIFFRACTION100
1.4004-1.4330.1971590.15982737X-RAY DIFFRACTION100
1.433-1.46880.18561700.14332717X-RAY DIFFRACTION100
1.4688-1.50850.17721380.12742734X-RAY DIFFRACTION100
1.5085-1.55290.15921520.12162722X-RAY DIFFRACTION100
1.5529-1.60310.17261470.1242762X-RAY DIFFRACTION100
1.6031-1.66040.14561590.12922731X-RAY DIFFRACTION100
1.6604-1.72680.16451250.12092772X-RAY DIFFRACTION100
1.7268-1.80540.16341390.12852768X-RAY DIFFRACTION100
1.8054-1.90060.14481640.12272758X-RAY DIFFRACTION100
1.9006-2.01970.13891400.12422753X-RAY DIFFRACTION100
2.0197-2.17560.16151500.1252760X-RAY DIFFRACTION100
2.1756-2.39450.14551280.13072779X-RAY DIFFRACTION99
2.3945-2.74090.16151310.14852805X-RAY DIFFRACTION99
2.7409-3.4530.1671440.15552795X-RAY DIFFRACTION99

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