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- PDB-8wlv: Crystal structure of P122A_Msd in complex with 5-azauracil -

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Basic information

Entry
Database: PDB / ID: 8wlv
TitleCrystal structure of P122A_Msd in complex with 5-azauracil
ComponentsCMP/dCMP deaminase, zinc-binding protein
KeywordsHYDROLASE / Mycobacterial deaminase / s-triazine deaminase / CDA
Function / homologyCytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / catalytic activity / metal ion binding / : / CMP/dCMP deaminase, zinc-binding protein
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPorathoor, S. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/NWBA/39/03/2018- 19 India
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Mechanism of deamination by mycobacterial deaminase selectively targeting mutagenic bases.
Authors: Porathoor, S. / Choudhury, A.R. / Chakrabarti, R. / Anand, R.
History
DepositionOct 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 16, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
C: CMP/dCMP deaminase, zinc-binding protein
D: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,69118
Polymers68,4254
Non-polymers1,26714
Water2,648147
1
A: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8469
Polymers34,2122
Non-polymers6337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-28 kcal/mol
Surface area13230 Å2
MethodPISA
2
C: CMP/dCMP deaminase, zinc-binding protein
D: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8469
Polymers34,2122
Non-polymers6337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-26 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.670, 109.470, 64.320
Angle α, β, γ (deg.)90.000, 98.957, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CMP/dCMP deaminase, zinc-binding protein


Mass: 17106.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEI_3493 / Production host: Escherichia coli (E. coli) / References: UniProt: I7G9Z0
#2: Chemical
ChemComp-WHC / 1~{H}-1,3,5-triazine-2,4-dione / 5-azauracil


Mass: 113.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate pH 5.6, 20% PEG 3000 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→55.01 Å / Num. obs: 51013 / % possible obs: 98.8 % / Redundancy: 3.69 % / CC1/2: 0.99 / Net I/σ(I): 11.37
Reflection shellResolution: 1.96→2.011 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 7446 / CC1/2: 0.85 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→55.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.818 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2234 2463 4.829 %
Rwork0.1901 48544 -
all0.192 --
obs-48544 98.824 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.452 Å2-0 Å20.853 Å2
2---2.87 Å2-0 Å2
3---2.909 Å2
Refinement stepCycle: LAST / Resolution: 1.96→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 72 147 4950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124916
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164474
X-RAY DIFFRACTIONr_angle_refined_deg1.451.6696707
X-RAY DIFFRACTIONr_angle_other_deg0.4881.58910213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.711550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09510667
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.13710212
X-RAY DIFFRACTIONr_chiral_restr0.0670.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
X-RAY DIFFRACTIONr_nbd_refined0.2230.21024
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.23953
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22417
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.22
X-RAY DIFFRACTIONr_metal_ion_refined0.140.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.219
X-RAY DIFFRACTIONr_nbd_other0.3070.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2760.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2320.22
X-RAY DIFFRACTIONr_mcbond_it2.5453.2012528
X-RAY DIFFRACTIONr_mcbond_other2.5373.2012528
X-RAY DIFFRACTIONr_mcangle_it3.4655.7383154
X-RAY DIFFRACTIONr_mcangle_other3.4665.7393155
X-RAY DIFFRACTIONr_scbond_it3.7113.5932388
X-RAY DIFFRACTIONr_scbond_other3.713.5932389
X-RAY DIFFRACTIONr_scangle_it5.5726.3943553
X-RAY DIFFRACTIONr_scangle_other5.5726.3943554
X-RAY DIFFRACTIONr_lrange_it6.6634.3975437
X-RAY DIFFRACTIONr_lrange_other6.66234.4085432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0110.3241830.33603X-RAY DIFFRACTION99.3962
2.011-2.0660.3361860.3043452X-RAY DIFFRACTION98.9663
2.066-2.1260.3371810.2953354X-RAY DIFFRACTION97.6519
2.126-2.1910.261720.2273334X-RAY DIFFRACTION99.7156
2.191-2.2630.3271820.3342988X-RAY DIFFRACTION94.4577
2.263-2.3420.2671550.2393100X-RAY DIFFRACTION98.816
2.342-2.430.241470.1883026X-RAY DIFFRACTION99.937
2.43-2.5290.2441540.1842870X-RAY DIFFRACTION99.1801
2.529-2.6410.2391320.1832809X-RAY DIFFRACTION99.7626
2.641-2.770.2441080.1742669X-RAY DIFFRACTION99.285
2.77-2.920.1781150.1652541X-RAY DIFFRACTION99.6249
2.92-3.0960.2141150.1682416X-RAY DIFFRACTION99.921
3.096-3.3090.2111090.1712239X-RAY DIFFRACTION99.1973
3.309-3.5730.2361070.1822066X-RAY DIFFRACTION98.9076
3.573-3.9130.181940.1611883X-RAY DIFFRACTION97.4852
3.913-4.3720.205940.1591755X-RAY DIFFRACTION99.2485
4.372-5.0430.156820.1451532X-RAY DIFFRACTION99.201
5.043-6.1630.156670.1661294X-RAY DIFFRACTION99.0539
6.163-8.6610.21490.1461028X-RAY DIFFRACTION98.6264
8.661-55.010.143310.175585X-RAY DIFFRACTION98.4026

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