[English] 日本語
Yorodumi
- PDB-9l29: YdiU in complex with NAD, short soaking experiment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l29
TitleYdiU in complex with NAD, short soaking experiment
ComponentsProtein adenylyltransferase SelO
KeywordsLYASE / YdiU / NAD
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / magnesium ion binding / ATP binding
Similarity search - Function
: / Protein adenylyltransferase SelO / Protein adenylyltransferase SelO
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Protein nucleotidyltransferase YdiU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLiu, K. / Zhang, T. / Wang, T. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82350116 China
CitationJournal: Cell / Year: 2026
Title: Hydrolyzing NAD to NMN and ADP by SelO required for Mitochondria Homeostasis
Authors: Jia, X. / Zhang, T. / Yang, C. / Liu, K. / Wu, L. / Diao, L. / Yang, Y. / Wu, J. / Li, Y. / Sun, W. / Zhang, K. / Jiang, Y. / Zhao, Y. / Zhang, X. / Jiang, P. / Jiang, Y. / Yu, Q. / Xiang, S. / Fu, Y. / Wang, T.
History
DepositionDec 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7604
Polymers55,9051
Non-polymers8563
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.560, 95.340, 118.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein adenylyltransferase SelO / YdiU


Mass: 55904.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: selO, BKL28_004258, HLZ39_02825 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2T1ME41, protein adenylyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 75 mM Tris (pH 8.5), 1.5 M ammonium sulfate, 25% glycerol (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→47.72 Å / Num. obs: 33367 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.232 / Rrim(I) all: 0.241 / Net I/σ(I): 10.48
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.05-2.13.24624200.5943.3761
2.1-2.162.26723970.7232.3581
2.16-2.221.61722660.7931.6841
2.22-2.291.27122460.8121.3231
2.29-2.371.02421750.8581.0661
2.37-2.450.83321120.9270.8671
2.45-2.540.81720380.9280.8491
2.54-2.650.64619480.9510.6721
2.65-2.760.51218680.9690.5331
2.76-2.90.38518090.9810.41
2.9-3.060.317300.9860.3131
3.06-3.240.20916230.9920.2181
3.24-3.470.14615430.9950.1521
3.47-3.740.10514240.9970.111
3.74-4.10.08513480.9980.0891
4.1-4.580.07212240.9980.0751
4.58-5.290.06810800.9980.0711
5.29-6.480.0759270.9980.0791
6.48-9.170.0557470.9990.0581
9.17-47.720.044420.9990.0421

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JYN

9jyn


Resolution: 2.05→47.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.629 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24229 1661 5 %RANDOM
Rwork0.19853 ---
obs0.20078 31646 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2---0.91 Å20 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.05→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 54 181 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123985
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163605
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.8265419
X-RAY DIFFRACTIONr_angle_other_deg0.5561.7628258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.252541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76710632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021018
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_it2.8611.9141907
X-RAY DIFFRACTIONr_mcbond_other1.9091.9181907
X-RAY DIFFRACTIONr_mcangle_it3.4073.4282382
X-RAY DIFFRACTIONr_mcangle_other3.4143.4332383
X-RAY DIFFRACTIONr_scbond_it3.352.1992078
X-RAY DIFFRACTIONr_scbond_other3.352.1952071
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3383.9273026
X-RAY DIFFRACTIONr_long_range_B_refined6.99419.074515
X-RAY DIFFRACTIONr_long_range_B_other6.99319.084516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 124 -
Rwork0.321 2293 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: -16.7382 Å / Origin y: -9.8143 Å / Origin z: 11.6302 Å
111213212223313233
T0.1661 Å2-0.0207 Å2-0.0014 Å2-0.3166 Å2-0.0041 Å2--0.012 Å2
L0.0228 °2-0.0694 °2-0.0226 °2-0.3576 °2-0.3089 °2--1.082 °2
S0.0118 Å °-0.017 Å °-0.0132 Å °0.0098 Å °0.0359 Å °0.0642 Å °-0.0148 Å °0.0077 Å °-0.0477 Å °

+
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