[English] 日本語
Yorodumi
- PDB-9jql: The C-terminal structure of N6-methyladenosine deaminase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jql
TitleThe C-terminal structure of N6-methyladenosine deaminase
ComponentsPutative adenine deaminase YerA
KeywordsMETAL BINDING PROTEIN / Epigenetic nucleoside deaminase / Metal-dependent hydrolases / YerA
Function / homology
Function and homology information


adenine deaminase / adenine deaminase activity / adenine catabolic process
Similarity search - Function
Adenine deaminase / Adenine deaminase C-terminal domain / Adenine deaminase C-terminal domain / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Putative adenine deaminase YerA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXie, W. / Jia, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022A1515011768 China
CitationJournal: Biochem.J. / Year: 2025
Title: The C-terminal structure of the N6-methyladenosine deaminase YerA and its role in deamination.
Authors: Jia, Q. / Zeng, H. / Xiao, N. / Tang, J. / Gao, S. / Xie, W.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative adenine deaminase YerA


Theoretical massNumber of molelcules
Total (without water)22,7171
Polymers22,7171
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.169, 103.169, 42.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Putative adenine deaminase YerA / Adenase / Adenine aminase


Mass: 22717.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yerA, yecB, BSU06560 / Production host: Escherichia coli (E. coli) / References: UniProt: O34909, adenine deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.5 M KH2PO4 and 0.1 M HEPES (pH7.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→23.76 Å / Num. obs: 13926 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.124 / Net I/σ(I): 18.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 13964 / CC1/2: 0.887 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→23.76 Å / SU ML: 0.1836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 668 4.8 %
Rwork0.2062 13258 -
obs0.2065 13926 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 101 1674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281603
X-RAY DIFFRACTIONf_angle_d0.60852162
X-RAY DIFFRACTIONf_chiral_restr0.0451244
X-RAY DIFFRACTIONf_plane_restr0.0046276
X-RAY DIFFRACTIONf_dihedral_angle_d17.265601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.27061370.2262587X-RAY DIFFRACTION100
2.26-2.490.27951050.23082646X-RAY DIFFRACTION100
2.49-2.850.24141420.22642608X-RAY DIFFRACTION99.96
2.85-3.590.21081340.212648X-RAY DIFFRACTION100
3.59-23.760.17421500.18422769X-RAY DIFFRACTION99.18

+
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