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- PDB-6j4t: Crystal structure of arabidopsis ADAL complexed with IMP -

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Basic information

Entry
Database: PDB / ID: 6j4t
TitleCrystal structure of arabidopsis ADAL complexed with IMP
ComponentsAdenosine/AMP deaminase family protein
KeywordsHYDROLASE / m6A / N6-mAMP / arabidopsis / Zn / GMP / complex / deaminase
Function / homology
Function and homology information


N6-methyl-AMP deaminase activity / toxic metabolite repair / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / inosine biosynthetic process / adenosine deaminase activity / adenosine catabolic process / nucleotide metabolic process / RNA catabolic process / chloroplast ...N6-methyl-AMP deaminase activity / toxic metabolite repair / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / inosine biosynthetic process / adenosine deaminase activity / adenosine catabolic process / nucleotide metabolic process / RNA catabolic process / chloroplast / metal ion binding / cytosol
Similarity search - Function
Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
INOSINIC ACID / N6-mAMP deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWu, B.X. / Zhang, D. / Nie, H.B. / Shen, S.L. / Li, S.S. / Patel, D.J.
CitationJournal: Rna Biol. / Year: 2019
Title: Structure ofArabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications forN6-methyl-AMP recognition and processing.
Authors: Wu, B. / Zhang, D. / Nie, H. / Shen, S. / Li, Y. / Li, S.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine/AMP deaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4163
Polymers40,0031
Non-polymers4142
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-26 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 81.921, 87.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenosine/AMP deaminase family protein / ADAL / Putative adenosine deaminase


Mass: 40002.715 Da / Num. of mol.: 1 / Mutation: D295N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g04880, T4B21.20, T4B21_20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LPL7
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 32042 / % possible obs: 96.8 % / Redundancy: 10.6 % / Net I/σ(I): 11.8
Reflection shellResolution: 1.82→1.92 Å / Rmerge(I) obs: 0.135

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J23

6j23


Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.82 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22896 1640 5.1 %RANDOM
Rwork0.18748 ---
obs0.18959 30324 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.82→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 24 185 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172661
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6343795
X-RAY DIFFRACTIONr_angle_other_deg1.4431.5776164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82122.014144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
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_it1.8842.1171367
X-RAY DIFFRACTIONr_mcbond_other1.8812.1141366
X-RAY DIFFRACTIONr_mcangle_it2.7383.1551707
X-RAY DIFFRACTIONr_mcangle_other2.7393.1591708
X-RAY DIFFRACTIONr_scbond_it2.6112.4271434
X-RAY DIFFRACTIONr_scbond_other2.6112.4271434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0813.5152089
X-RAY DIFFRACTIONr_long_range_B_refined6.16826.2183207
X-RAY DIFFRACTIONr_long_range_B_other6.14326.1213184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 136 -
Rwork0.2 2238 -
obs--98.79 %

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