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- PDB-6ijm: Apo structure of the N6-methyl-AMP Deaminase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6ijm
TitleApo structure of the N6-methyl-AMP Deaminase from Arabidopsis thaliana
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.016 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,5592
Polymers42,4931
Non-polymers651
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.625, 79.862, 86.853
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: 42493.438 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26-36% PEG 3350, 0.2 M NaCl, 0.1 M HEPEs (pH 7.5)

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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: 2→50 Å / Num. obs: 23673 / % possible obs: 98.7 % / Observed criterion σ(I): 2.9 / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2287 / CC1/2: 0.876 / % possible all: 98.7

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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

2ada


Resolution: 2.016→43.737 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.2221 1165 5.25 %
Rwork0.1743 --
obs0.1768 22196 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.016→43.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 1 193 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112667
X-RAY DIFFRACTIONf_angle_d0.9233606
X-RAY DIFFRACTIONf_dihedral_angle_d15.3321605
X-RAY DIFFRACTIONf_chiral_restr0.055425
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0157-2.10740.2626930.19941706X-RAY DIFFRACTION61
2.1074-2.21850.26421600.1932436X-RAY DIFFRACTION89
2.2185-2.35750.25591440.19942762X-RAY DIFFRACTION99
2.3575-2.53950.2251250.18172816X-RAY DIFFRACTION99
2.5395-2.7950.22781810.18112736X-RAY DIFFRACTION98
2.795-3.19930.23751480.17832799X-RAY DIFFRACTION99
3.1993-4.03040.20821550.15892828X-RAY DIFFRACTION99
4.0304-43.74770.19721590.16482948X-RAY DIFFRACTION98

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