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- PDB-9jym: YdiU complexed with NAD and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 9jym
TitleYdiU complexed with NAD and Mn2+
ComponentsProtein adenylyltransferase SelO
KeywordsTRANSFERASE / Complex
Function / homologyADENOSINE MONOPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
DepositionOct 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5916
Polymers55,9051
Non-polymers6865
Water10,737596
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.725, 95.722, 119.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein adenylyltransferase SelO


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: protein adenylyltransferase

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Non-polymers , 5 types, 601 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 75 mM Tris (pH8.5), 1.5M ammonium sulfate, 25% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979191 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.07→39.77 Å / Num. obs: 32400 / % possible obs: 98.9 % / Redundancy: 10.9 % / CC1/2: 0.996 / Net I/σ(I): 17.4
Reflection shellResolution: 2.07→2.12 Å / Num. unique obs: 2121 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
xia2data reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNA

6lna


Resolution: 2.07→37.33 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 1600 4.96 %
Rwork0.1513 --
obs0.1533 32226 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 40 596 4464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063981
X-RAY DIFFRACTIONf_angle_d0.8495406
X-RAY DIFFRACTIONf_dihedral_angle_d16.0471456
X-RAY DIFFRACTIONf_chiral_restr0.049568
X-RAY DIFFRACTIONf_plane_restr0.007705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.140.2281190.14552430X-RAY DIFFRACTION88
2.14-2.210.22541200.16482704X-RAY DIFFRACTION96
2.21-2.30.30751440.21442744X-RAY DIFFRACTION100
2.3-2.410.18111550.14912816X-RAY DIFFRACTION100
2.41-2.530.22961360.15122803X-RAY DIFFRACTION100
2.53-2.690.20421440.15292791X-RAY DIFFRACTION100
2.69-2.90.1891570.15022798X-RAY DIFFRACTION100
2.9-3.190.2161330.14542836X-RAY DIFFRACTION100
3.19-3.650.14491660.13292823X-RAY DIFFRACTION100
3.65-4.60.14991550.12432884X-RAY DIFFRACTION100
4.6-37.330.18891710.17052997X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11660.01830.04570.10920.00460.12710.00390.0164-0.0055-0.01180.0004-0.01540.0207-0.0031-0.0250.0086-0.001-0.00550.01330.00390.0137-7.3163-16.1821-17.7551
20.2-0.0233-0.05430.14850.10110.4837-0.01160.0010.0586-0.00910.00080.0211-0.1029-0.0142-0.22580.04870.00510.00110.0321-0.00490.0449-3.79464.49351.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 332 )
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 478 )

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