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- PDB-9jyn: YdiU complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 9jyn
TitleYdiU complexed with NAD
ComponentsProtein adenylyltransferase SelO
KeywordsTRANSFERASE / Complex
Function / homologyADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)56,4444
Polymers55,9051
Non-polymers5393
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.990, 96.040, 119.300
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 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
#2: 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
#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.: 267 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 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: 1.7→50 Å / Num. obs: 57854 / % possible obs: 97 % / Redundancy: 6.75 % / CC1/2: 0.996 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 6.69 % / Num. unique obs: 8235 / CC1/2: 0.506 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNA

6lna


Resolution: 1.7→39.21 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.948 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24854 2819 5 %RANDOM
Rwork0.22683 ---
obs0.22794 53763 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2--0.57 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.7→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 33 267 4133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123963
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163605
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.825382
X-RAY DIFFRACTIONr_angle_other_deg0.5831.7618255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.243540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10510634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021014
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_it1.7321.7351910
X-RAY DIFFRACTIONr_mcbond_other1.7251.7361910
X-RAY DIFFRACTIONr_mcangle_it2.6653.1062384
X-RAY DIFFRACTIONr_mcangle_other2.6653.112385
X-RAY DIFFRACTIONr_scbond_it2.5062.0362053
X-RAY DIFFRACTIONr_scbond_other2.4872.0322045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.983.5972987
X-RAY DIFFRACTIONr_long_range_B_refined6.16418.044485
X-RAY DIFFRACTIONr_long_range_B_other6.16418.054486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 235 -
Rwork0.263 4040 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.1243 Å / Origin y: -9.8747 Å / Origin z: -11.7393 Å
111213212223313233
T0.0341 Å20.0103 Å20.0023 Å2-0.0035 Å20.001 Å2--0.0078 Å2
L0.3586 °20.1921 °20.0901 °2-0.5552 °20.2412 °2--1.0595 °2
S-0.0032 Å °0.0062 Å °0.0384 Å °-0.0051 Å °0.009 Å °-0.019 Å °-0.0499 Å °0.0023 Å °-0.0058 Å °

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