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- PDB-9lq9: Crysral structure of NrN -

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Basic information

Entry
Database: PDB / ID: 9lq9
TitleCrysral structure of NrN
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: 2.38 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

Downloads & links

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Assembly

Deposited unit
A: NrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0552
Polymers30,0001
Non-polymers551
Water48627
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)112.270, 112.270, 40.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NrN


Mass: 30000.117 Da / Num. of mol.: 1
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, FSA06_24365, NXX45_16660
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9V7I2
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% v/v 2-Propanol, 0.1 M BICINE pH 8.5, 30% w/v Polyethylene glycol 1,500

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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: 2.38→36.75 Å / Num. obs: 11819 / % possible obs: 99.9 % / Redundancy: 19.3 % / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 860 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→36.75 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 583 4.94 %
Rwork0.2001 --
obs0.2018 11800 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 1 27 2023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012035
X-RAY DIFFRACTIONf_angle_d1.2962760
X-RAY DIFFRACTIONf_dihedral_angle_d6.127269
X-RAY DIFFRACTIONf_chiral_restr0.067310
X-RAY DIFFRACTIONf_plane_restr0.009356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.30191660.2852734X-RAY DIFFRACTION100
2.62-30.25651360.21422804X-RAY DIFFRACTION100
3-3.780.2581430.232790X-RAY DIFFRACTION100
3.78-36.750.20851380.17192889X-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)
14.9384-0.09760.81385.5075-0.53583.30010.03760.17490.3918-0.8866-0.03950.1462-0.00270.0248-0.04490.57340.0351-0.01770.5101-0.02780.542121.9774-27.7404-1.0639
24.13150.589-2.17852.2342-1.32022.9620.150.04350.4284-0.1578-0.05460.0322-0.09480.0627-0.11990.41910.0176-0.07790.3985-0.07220.391449.9077-17.1868-1.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 259 )

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