[English] 日本語
Yorodumi
- PDB-6iv5: Crystal structure of arabidopsis N6-mAMP deaminase MAPDA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iv5
TitleCrystal structure of arabidopsis N6-mAMP deaminase MAPDA
ComponentsAdenosine/AMP deaminase family protein
KeywordsHYDROLASE / m6A / N6-mAMP / arabidopsis / Zn
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
PHOSPHATE ION / N6-mAMP deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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
DepositionDec 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,1643
Polymers40,0041
Non-polymers1602
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.904, 82.352, 86.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 40003.699 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8M Potassium phosphate (dibasic), 0.1M HEPES/Sodium hydroxide, 0.8M Sodium phosphate (monobasic)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 1.748→59.71 Å / Num. obs: 37600 / % possible obs: 95.6 % / Redundancy: 13 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.1
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.085 / Num. unique obs: 5414

-
Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4M

1a4m


Resolution: 1.749→29.853 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.61
RfactorNum. reflection% reflection
Rfree0.2179 1808 5.03 %
Rwork0.1879 --
obs0.1893 35912 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.749→29.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 6 125 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062737
X-RAY DIFFRACTIONf_angle_d0.8763702
X-RAY DIFFRACTIONf_dihedral_angle_d12.0331659
X-RAY DIFFRACTIONf_chiral_restr0.059436
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7485-1.79580.28621390.23752715X-RAY DIFFRACTION100
1.7958-1.84860.27051510.20822671X-RAY DIFFRACTION100
1.8486-1.90830.24721490.20042702X-RAY DIFFRACTION100
1.9083-1.97650.23921390.18632706X-RAY DIFFRACTION100
1.9765-2.05560.21581370.192596X-RAY DIFFRACTION99
2.0556-2.14910.2849830.191802X-RAY DIFFRACTION99
2.1491-2.26240.22691280.18922279X-RAY DIFFRACTION99
2.2624-2.40410.21531400.19662691X-RAY DIFFRACTION100
2.4041-2.58960.23941740.19482696X-RAY DIFFRACTION100
2.5896-2.850.24541530.20632743X-RAY DIFFRACTION100
2.85-3.2620.21391520.20212750X-RAY DIFFRACTION100
3.262-4.10810.21261400.1742801X-RAY DIFFRACTION100
4.1081-29.85690.17161230.17222952X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more