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- PDB-8wlx: Crystal structure of P123A_Msd -

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Basic information

Entry
Database: PDB / ID: 8wlx
TitleCrystal structure of P123A_Msd
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 / ACETATE ION / CMP/dCMP deaminase, zinc-binding protein
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.562 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,19814
Polymers34,2122
Non-polymers98612
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-102 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.660, 108.560, 53.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 17106.154 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH 6.4, 0.2M Mg-acetate tetrahydrate, 20% PEG 8000

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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: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→19.763 Å / Num. obs: 53097 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.99 / Net I/σ(I): 16.79
Reflection shellResolution: 1.562→1.602 Å / Num. unique obs: 3769 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.562→19.763 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.155 / SU B: 1.67 / SU ML: 0.057 / Average fsc free: 0.9689 / Average fsc work: 0.9757 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1932 967 1.824 %
Rwork0.1703 52049 -
all0.171 --
obs-53016 99.896 %
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: 18.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å2-0 Å2-0 Å2
2---0.023 Å20 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.562→19.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 58 245 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162359
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.8123484
X-RAY DIFFRACTIONr_angle_other_deg0.6641.7565400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.213528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75910356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97610113
X-RAY DIFFRACTIONr_chiral_restr0.0890.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023139
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02609
X-RAY DIFFRACTIONr_nbd_refined0.220.2514
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22091
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21230
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2178
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.29
X-RAY DIFFRACTIONr_nbd_other0.1550.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.232
X-RAY DIFFRACTIONr_mcbond_it1.6531.7781296
X-RAY DIFFRACTIONr_mcbond_other1.6321.7751294
X-RAY DIFFRACTIONr_mcangle_it2.463.1881619
X-RAY DIFFRACTIONr_mcangle_other2.4653.191620
X-RAY DIFFRACTIONr_scbond_it3.0632.1821260
X-RAY DIFFRACTIONr_scbond_other3.0622.1841261
X-RAY DIFFRACTIONr_scangle_it4.5183.7921860
X-RAY DIFFRACTIONr_scangle_other4.5173.7941861
X-RAY DIFFRACTIONr_lrange_it5.73220.4932877
X-RAY DIFFRACTIONr_lrange_other5.67119.092822
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
1.562-1.6020.284690.26737690.26738390.9460.94799.9740.237
1.602-1.6460.23650.2436680.2437340.9530.95999.97320.205
1.646-1.6930.245920.23235800.23336750.9610.96399.91840.196
1.693-1.7450.258520.21334780.21335300.9570.9681000.176
1.745-1.8020.247630.20233910.20334540.960.9721000.166
1.802-1.8640.23640.19132710.19233360.9640.97699.970.154
1.864-1.9340.202570.17731750.17832330.9710.97999.96910.142
1.934-2.0120.2600.16230490.16231090.9760.9831000.133
2.012-2.1010.22480.16629390.16729880.9720.98399.96650.141
2.101-2.2020.199490.1628210.1628710.9750.98499.96520.134
2.202-2.320.182390.15126840.15227230.980.9861000.128
2.32-2.4580.186610.15525280.15525890.980.9851000.133
2.458-2.6250.181470.15324020.15324490.9830.9851000.135
2.625-2.8310.198480.15422360.15522840.9720.9851000.139
2.831-3.0950.206350.16120930.16121280.9750.9851000.15
3.095-3.450.181320.16318840.16319180.9740.98499.89570.159
3.45-3.9640.162340.14816900.14817280.9890.98799.76850.155
3.964-4.8060.099230.14514580.14414810.9950.9881000.156
4.806-6.6050.291160.18611840.18812000.9740.9831000.195
6.605-19.7630.149130.1857490.1847640.9870.9899.73820.209

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