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- PDB-9wbu: Crystal structure of Mtb cyclic dinucleotide phosphodiesterase by... -

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Basic information

Entry
Database: PDB / ID: 9wbu
TitleCrystal structure of Mtb cyclic dinucleotide phosphodiesterase by sulfur-modified cyclic dinucleotide analogue
ComponentsBifunctional oligoribonuclease and PAP phosphatase NrnA
KeywordsHYDROLASE / Bifunctional oligoribonuclease and PAP phosphatase NrnA
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
: / : / Bifunctional oligoribonuclease and PAP phosphatase NrnA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsHanuman, S.D. / Rajakumara, E.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003946 India
CitationJournal: Rsc Chem Biol / Year: 2026
Title: Structural and biochemical insights into the inhibition of Mycobacterium tuberculosis cyclic dinucleotide phosphodiesterase by a sulfur-modified cyclic dinucleotide analog.
Authors: Hanuman, D.S. / Neeharika, S. / Murari, S.K. / Yeboah, S.K. / Sintim, H.O. / Rajakumara, E.
History
DepositionAug 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,61910
Polymers106,3693
Non-polymers2,2507
Water00
1
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4337
Polymers70,9122
Non-polymers1,5215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-14 kcal/mol
Surface area22480 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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area3760 Å2
ΔGint-14 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.010, 149.096, 167.033
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 / Mutation: NO
Source method: isolated from a genetically manipulated source
Details: Recombinantly purified c-di-NMP Phosphodiesterase (CdnP) of Mycobacterium tuberculosis
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: nrnA, Rv2837c / Plasmid: pET28c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P71615, Hydrolases; Acting on ester bonds, 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical ChemComp-A1MBE / (1~{R},6~{S},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,7,11,13,16-pentaoxa-4-thia-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecane-9,18-diol


Mass: 674.477 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N10O11P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 0.1 M Sodium Acetate Trihydrate pH 4.5, 2M Sodium Formate (30 % Ethylene Glycol)
PH range: 4.5 - 5.5

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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: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.96→51.63 Å / Num. obs: 20959 / % possible obs: 99.86 % / Redundancy: 5.1 % / Biso Wilson estimate: 49.73 Å2 / CC1/2: 0.965 / CC star: 0.991 / Net I/σ(I): 4.8
Reflection shellResolution: 2.96→3.14 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.29 / Num. unique obs: 3344 / CC1/2: 0.73 / Rpim(I) all: 0.63 / Rrim(I) all: 0.39 / Χ2: 0.37 / % possible all: 99.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→25.23 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / SU B: 27.935 / SU ML: 0.478 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27017 1036 5 %RANDOM
Rwork0.21817 ---
obs0.22081 19835 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å2-0 Å2
2---3.27 Å20 Å2
3---2.59 Å2
Refinement stepCycle: 1 / Resolution: 2.96→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6909 0 3 0 6912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166616
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.7919635
X-RAY DIFFRACTIONr_angle_other_deg0.4781.72815124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.082552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67610984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021505
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_it3.6924.8713735
X-RAY DIFFRACTIONr_mcbond_other3.694.8713734
X-RAY DIFFRACTIONr_mcangle_it5.9868.7414648
X-RAY DIFFRACTIONr_mcangle_other5.9868.744649
X-RAY DIFFRACTIONr_scbond_it3.3524.9743301
X-RAY DIFFRACTIONr_scbond_other3.3524.9743302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5759.0984988
X-RAY DIFFRACTIONr_long_range_B_refined8.39744.537755
X-RAY DIFFRACTIONr_long_range_B_other8.39944.537756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.96→3.036 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 77 -
Rwork0.32 1440 -
obs--99.93 %

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