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- PDB-9lqc: Crystal structure of NrN D119A in complex with SAH-AMP -

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Basic information

Entry
Database: PDB / ID: 9lqc
TitleCrystal structure of NrN D119A in complex with SAH-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: 2.37 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
B: NrN
C: NrN
D: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6798
Polymers119,8244
Non-polymers2,8544
Water7,891438
1
A: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6702
Polymers29,9561
Non-polymers7141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6702
Polymers29,9561
Non-polymers7141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6702
Polymers29,9561
Non-polymers7141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6702
Polymers29,9561
Non-polymers7141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.668, 121.609, 72.579
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NrN


Mass: 29956.109 Da / Num. of mol.: 4 / Mutation: D119A
Source method: isolated from a genetically manipulated source
Details: deletions / Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: CQW34_02202, F2Z29_06630, F2Z89_11900, F3B44_04915, FSA03_20595, NXX45_16660
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9V7I2
#2: Chemical
ChemComp-A1EL0 / (2~{S})-4-[[(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]methylsulfanyl]-2-azanyl-butanoic acid


Mass: 713.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H32N11O11PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Succinic acid pH 7.0, 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: 2.37→72.73 Å / Num. obs: 46516 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.83 / Net I/σ(I): 4
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 3422 / CC1/2: 0.235

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→72.58 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 2511 5.41 %
Rwork0.2548 --
obs0.2569 46423 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→72.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 192 438 8794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.752
X-RAY DIFFRACTIONf_dihedral_angle_d17.1423229
X-RAY DIFFRACTIONf_chiral_restr0.0491305
X-RAY DIFFRACTIONf_plane_restr0.0051471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.420.38921300.31242237X-RAY DIFFRACTION92
2.42-2.470.30671390.3012471X-RAY DIFFRACTION100
2.47-2.520.33821430.28782424X-RAY DIFFRACTION100
2.52-2.580.36931440.30022424X-RAY DIFFRACTION100
2.58-2.650.3431630.29582393X-RAY DIFFRACTION100
2.65-2.720.33351340.28562447X-RAY DIFFRACTION100
2.72-2.80.32111580.28132443X-RAY DIFFRACTION100
2.8-2.890.32381610.27822446X-RAY DIFFRACTION100
2.89-2.990.31661190.27762449X-RAY DIFFRACTION100
2.99-3.110.33011300.27582433X-RAY DIFFRACTION100
3.11-3.250.30721230.26412470X-RAY DIFFRACTION100
3.25-3.420.31151030.25392486X-RAY DIFFRACTION100
3.42-3.640.24631250.23622513X-RAY DIFFRACTION100
3.64-3.920.25871380.22242458X-RAY DIFFRACTION100
3.92-4.310.22121460.20162446X-RAY DIFFRACTION100
4.31-4.940.2611560.20712432X-RAY DIFFRACTION100
4.94-6.220.25951490.23722462X-RAY DIFFRACTION100
6.22-72.580.23591500.22372478X-RAY DIFFRACTION99

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