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- PDB-9lqa: Crystal structure of NrN E21A in complex with SAM-AMP -

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Basic information

Entry
Database: PDB / ID: 9lqa
TitleCrystal structure of NrN E21A in complex with SAM-AMP
ComponentsNrN
KeywordsIMMUNE SYSTEM / enzyme / phosphodiesterase / CRISPR-Cas system / second messenger
Function / homology: / : / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDuan, B. / Zhao, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.
Authors: Duan, B. / Zhao, B.
History
DepositionJan 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8484
Polymers29,9421
Non-polymers9063
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.396, 71.396, 121.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

21A-549-

HOH

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Components

#1: Protein NrN


Mass: 29942.082 Da / Num. of mol.: 1 / Mutation: E21A
Source method: isolated from a genetically manipulated source
Details: deletion / Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: CQW34_02202 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9V7I2
#2: Chemical ChemComp-A1EL3 / [(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium


Mass: 728.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N11O11PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 153 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2024
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.91→121.5 Å / Num. obs: 25179 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 0.998 / Net I/σ(I): 14
Reflection shellResolution: 1.91→1.96 Å / Num. unique obs: 1810 / CC1/2: 0.391

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→50.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1258 5.01 %
Rwork0.1965 --
obs0.1985 25097 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 58 203 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.034
X-RAY DIFFRACTIONf_dihedral_angle_d19.038808
X-RAY DIFFRACTIONf_chiral_restr0.06326
X-RAY DIFFRACTIONf_plane_restr0.007367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.990.32331440.29482599X-RAY DIFFRACTION100
1.99-2.080.25141340.22912579X-RAY DIFFRACTION100
2.08-2.190.25881440.21232590X-RAY DIFFRACTION100
2.19-2.320.25251260.22232618X-RAY DIFFRACTION100
2.32-2.50.24021390.20142612X-RAY DIFFRACTION100
2.5-2.750.22871520.2032645X-RAY DIFFRACTION100
2.75-3.150.23981430.20312642X-RAY DIFFRACTION100
3.15-3.970.23821460.17772694X-RAY DIFFRACTION100
3.97-50.480.19331300.16652860X-RAY DIFFRACTION100

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