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- PDB-9ueo: Co-crystal structure of Mtb CdnP with arabinose-derived 2'3'-cGAM... -

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Basic information

Entry
Database: PDB / ID: 9ueo
TitleCo-crystal structure of Mtb CdnP with arabinose-derived 2'3'-cGAMP (AR-cGAMP) analogue
ComponentsBifunctional oligoribonuclease and PAP phosphatase NrnA
KeywordsHYDROLASE / Mycobacterium tuberculosis CdnP Inhibitor
Function / homology
Function and homology information


3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding
Similarity search - Function
: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Chem-9UH / : / Bifunctional oligoribonuclease and PAP phosphatase NrnA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHanuman, S.D. / Nitin, K. / Rajakumara, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2026
Title: Structural and Biochemical Insights into the Arabinose and Xylose Derivatives of Cyclic-GAMP-Mediated Inhibition of Mycobacterium tuberculosis Cyclic-di-AMP Phosphodiesterase.
Authors: Hanuman, D.S. / Neeharika, S. / Nitin, K. / Abhishek, S. / Sinha, K.M. / Rajakumara, E.
History
DepositionApr 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,61910
Polymers106,3693
Non-polymers2,2507
Water1,38777
1
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4337
Polymers70,9122
Non-polymers1,5215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-17 kcal/mol
Surface area22490 Å2
MethodPISA
2
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules

C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3716
Polymers70,9122
Non-polymers1,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455-x-1,-y+1/2,z1
Buried area3920 Å2
ΔGint-12 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 148.920, 159.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Bifunctional oligoribonuclease and PAP phosphatase NrnA / 3'(2') / 5'-bisphosphate nucleotidase / 3'-phosphoadenosine 5'-phosphate phosphatase / PAP ...3'(2') / 5'-bisphosphate nucleotidase / 3'-phosphoadenosine 5'-phosphate phosphatase / PAP phosphatase / nanoRNase


Mass: 35456.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: nrnA, Rv2837c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P71615, Hydrolases; Acting on ester bonds, 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical ChemComp-9UH / (2R,5R,7R,8S,10R,12aR,14R,15R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxyoctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione


Mass: 674.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: tacsimate pH 6.0 (6 % v/v), 10 mM MES monohydrate pH 6.0, polyethylene glycol 4000 (25 % w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→51.14 Å / Num. obs: 29097 / % possible obs: 99.83 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.68 Å2 / CC1/2: 0.98 / CC star: 0.99 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.22 / Χ2: 0.75 / Net I/σ(I): 4.96
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.412 / Num. unique obs: 2906 / CC1/2: 0.7 / CC star: 0.9 / R split: 0.9 / Rpim(I) all: 0.412 / Rrim(I) all: 0.583 / Χ2: 0.36 / % possible all: 99.83

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimless7data scaling
iMOSFLM7.1data reduction
REFMAC5refinement
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→51.14 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.25 1388 -
Rwork0.21 --
obs-29097 99.83 %
Displacement parametersBiso mean: 49.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6926 0 142 77 7145

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