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- PDB-8qou: Reactive intermediate deaminase A mutant - R107K -

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Basic information

Entry
Database: PDB / ID: 8qou
TitleReactive intermediate deaminase A mutant - R107K
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 / organonitrogen compound catabolic process / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity, producing 3'-phosphomonoesters / Hydrolases; Acting on ester bonds ...2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / organonitrogen compound catabolic process / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity, producing 3'-phosphomonoesters / 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: 1.4 Å
AuthorsRizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: To Be Published
Title: Reactive intermediate deaminase A mutant - R107K
Authors: Rizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S.
History
DepositionSep 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4136
Polymers29,1272
Non-polymers2864
Water6,125340
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)44,37212
Polymers43,6913
Non-polymers6819
Water543
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
Buried area7860 Å2
ΔGint-79 kcal/mol
Surface area15680 Å2
MethodPISA
2
B: 2-iminobutanoate/2-iminopropanoate deaminase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)43,8676
Polymers43,6913
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8250 Å2
ΔGint-76 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.482, 90.482, 90.482
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-305-

HOH

21A-462-

HOH

31A-477-

HOH

41B-544-

HOH

51B-629-

HOH

61B-641-

HOH

71B-647-

HOH

81B-651-

HOH

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Components

#1: Protein 2-iminobutanoate/2-iminopropanoate deaminase / 14.3 kDa perchloric acid soluble protein / Translation inhibitor L-PSP ribonuclease / UK114 antigen


Mass: 14563.620 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-iminobutanoate/2-iminopropanoate deaminase, Hydrolases; Acting on ester bonds
#2: 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
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate, pH 6.5, 30% w/v polyethylene glycol 8000

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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: 1.4→45.24 Å / Num. obs: 48575 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.939 / Net I/σ(I): 17.4
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2408 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.512 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17033 2432 5 %RANDOM
Rwork0.14935 ---
obs0.15042 46142 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.4→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 340 2375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162096
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6322882
X-RAY DIFFRACTIONr_angle_other_deg0.5441.5614839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.44158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42210352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
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_it0.9041.0131122
X-RAY DIFFRACTIONr_mcbond_other0.9011.0131122
X-RAY DIFFRACTIONr_mcangle_it1.2981.8321404
X-RAY DIFFRACTIONr_mcangle_other1.2971.8331405
X-RAY DIFFRACTIONr_scbond_it1.1531.247993
X-RAY DIFFRACTIONr_scbond_other1.1531.248994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4912.1791469
X-RAY DIFFRACTIONr_long_range_B_refined2.75615.672290
X-RAY DIFFRACTIONr_long_range_B_other2.10411.812213
X-RAY DIFFRACTIONr_rigid_bond_restr3.72434211
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 160 -
Rwork0.154 3445 -
obs--100 %

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