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- PDB-8wlw: Crystal structure of DelP123_Msd in complex with 5-azauracil -

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Basic information

Entry
Database: PDB / ID: 8wlw
TitleCrystal structure of DelP123_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 / : / CMP/dCMP deaminase, zinc-binding protein
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 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
C: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
D: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22316
Polymers68,1404
Non-polymers1,08212
Water5,531307
1
A: CMP/dCMP deaminase, zinc-binding protein
B: CMP/dCMP deaminase, zinc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6118
Polymers34,0702
Non-polymers5416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-26 kcal/mol
Surface area12960 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)34,6118
Polymers34,0702
Non-polymers5416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-28 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.750, 85.300, 76.460
Angle α, β, γ (deg.)90.000, 102.491, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17035.076 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.: 4 / Source method: obtained synthetically / 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.: 307 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.4, 20% PEG 1500

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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: 1.538→74.66 Å / Num. obs: 86243 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 0.99 / Net I/σ(I): 11.69
Reflection shellResolution: 1.538→1.578 Å / Num. unique obs: 6110 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.538→74.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.641 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2087 4298 4.984 %
Rwork0.1763 81941 -
all0.178 --
obs-86239 99.218 %
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: 17.242 Å2
Baniso -1Baniso -2Baniso -3
1-1.645 Å2-0 Å2-0.775 Å2
2---0.781 Å2-0 Å2
3----0.474 Å2
Refinement stepCycle: LAST / Resolution: 1.538→74.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 60 307 5086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164461
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.6696691
X-RAY DIFFRACTIONr_angle_other_deg0.5461.5910202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.346548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52310679
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.56810216
X-RAY DIFFRACTIONr_chiral_restr0.080.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021166
X-RAY DIFFRACTIONr_nbd_refined0.2370.21004
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24058
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22448
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4420.220
X-RAY DIFFRACTIONr_nbd_other0.310.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.211
X-RAY DIFFRACTIONr_mcbond_it1.6381.6432510
X-RAY DIFFRACTIONr_mcbond_other1.6191.6422509
X-RAY DIFFRACTIONr_mcangle_it2.3512.953134
X-RAY DIFFRACTIONr_mcangle_other2.3512.953135
X-RAY DIFFRACTIONr_scbond_it2.8011.9942392
X-RAY DIFFRACTIONr_scbond_other2.8011.9942393
X-RAY DIFFRACTIONr_scangle_it4.2933.4723557
X-RAY DIFFRACTIONr_scangle_other4.2923.4723558
X-RAY DIFFRACTIONr_lrange_it4.98617.7985477
X-RAY DIFFRACTIONr_lrange_other4.95917.445429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.538-1.5780.2752990.24261100.24364190.930.94699.84420.222
1.578-1.6210.2412990.21459510.21662500.950.9591000.19
1.621-1.6680.2053220.18457550.18560810.9660.97299.93420.163
1.668-1.7190.2273080.18255480.18458750.9630.97599.67660.162
1.719-1.7760.1962570.16453800.16557200.9720.9898.5490.144
1.776-1.8380.2022760.15552420.15755190.9730.98399.98190.138
1.838-1.9070.2342780.19149810.19353580.9620.97598.15230.169
1.907-1.9850.2242380.21347800.21351490.9650.9697.45580.194
1.985-2.0730.2482470.21546080.21749190.9310.9698.69890.2
2.073-2.1740.2022140.16644390.16747190.9730.98298.60140.154
2.174-2.2920.2352180.20841610.20944780.9580.96797.78920.197
2.292-2.4310.1952220.15740140.15942740.9770.98599.11090.155
2.431-2.5980.1912060.15437860.15639930.980.98699.9750.154
2.598-2.8060.1981920.16234920.16336970.9770.98499.64840.167
2.806-3.0740.2221690.16532630.16734420.9710.98399.70950.174
3.074-3.4360.1921420.16329640.16431100.9770.98499.87140.176
3.436-3.9660.1891410.16325730.16527350.980.98599.23220.183
3.966-4.8540.1711290.15822020.15923360.9850.98699.7860.189
4.854-6.8490.234960.18617220.18818200.9750.98399.89010.22
6.849-74.650.216450.1859700.18610250.980.98499.02440.234

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