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- PDB-6ijn: The D295N mutant of the N6-methyl-AMP deaminase from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 6ijn
TitleThe D295N mutant of the N6-methyl-AMP deaminase from Arabidopsis thaliana complexed with N6m-AMP
ComponentsAdenosine/AMP deaminase family protein
KeywordsHYDROLASE / Purine metabolism / deaminase / N6-methyladensosine / Tim-barrel / inosine / epigenetics
Function / homology
Function and homology information


N6-methyl-AMP deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / nucleotide metabolic process / RNA catabolic process / metal ion binding / cytosol
Similarity search - Function
Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
N6-METHYLADENOSINE-5'-MONOPHOSPHATE / N6-mAMP deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsXie, W. / Jia, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870782 China
National Natural Science Foundation of China31700657 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase.
Authors: Jia, Q. / Xie, W.
History
DepositionOct 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,8542
Polymers42,4921
Non-polymers3611
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-3 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.912, 80.086, 86.792
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 / Putative adenosine deaminase


Mass: 42492.453 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-6MZ / N6-METHYLADENOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 361.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% PEG 3350, 0.1 M NaCl, 0.1 M Tris-HCl (pH 9.0).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 42279 / % possible obs: 99.7 % / Observed criterion σ(I): 0.051 / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 13 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4139 / CC1/2: 0.959 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ADA
Resolution: 1.66→43.268 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.58
RfactorNum. reflection% reflection
Rfree0.1741 2141 5.1 %
Rwork0.1474 --
obs0.1487 42004 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→43.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 24 305 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092769
X-RAY DIFFRACTIONf_angle_d1.0653754
X-RAY DIFFRACTIONf_dihedral_angle_d17.7591662
X-RAY DIFFRACTIONf_chiral_restr0.069444
X-RAY DIFFRACTIONf_plane_restr0.007471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6546-1.69310.21871380.1732500X-RAY DIFFRACTION95
1.6931-1.73540.20541360.1662632X-RAY DIFFRACTION99
1.7354-1.78230.191480.16342629X-RAY DIFFRACTION100
1.7823-1.83480.18831480.15082579X-RAY DIFFRACTION100
1.8348-1.8940.19491490.15112605X-RAY DIFFRACTION99
1.894-1.96170.19951550.14732646X-RAY DIFFRACTION100
1.9617-2.04020.16771610.13522600X-RAY DIFFRACTION100
2.0402-2.13310.14521420.13882658X-RAY DIFFRACTION100
2.1331-2.24550.17231370.14182672X-RAY DIFFRACTION100
2.2455-2.38620.17471360.14232669X-RAY DIFFRACTION100
2.3862-2.57040.15511220.13952686X-RAY DIFFRACTION100
2.5704-2.82910.1891390.14692678X-RAY DIFFRACTION100
2.8291-3.23830.14861480.14282697X-RAY DIFFRACTION100
3.2383-4.07950.17131290.13722753X-RAY DIFFRACTION100
4.0795-43.28240.1741530.1622859X-RAY DIFFRACTION100

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