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- PDB-7c3u: Crystal structure of NE0047 (N66A) mutant in complex with 8-azaguanine -

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Basic information

Entry
Database: PDB / ID: 7c3u
TitleCrystal structure of NE0047 (N66A) mutant in complex with 8-azaguanine
ComponentsCytidine and deoxycytidylate deaminase zinc-binding region
KeywordsHYDROLASE / DEAMINASE / 8-AZAGUANINE / COMPLEX
Function / homology
Function and homology information


guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL / Cytidine and deoxycytidylate deaminase zinc-binding region
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGaded, V. / Bitra, A. / Singh, J. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentEMR/2015/ 002121 India
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structure guided mutagenesis reveals the substrate determinants of guanine deaminase.
Authors: Singh, J. / Gaded, V. / Bitra, A. / Anand, R.
History
DepositionMay 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytidine and deoxycytidylate deaminase zinc-binding region
B: Cytidine and deoxycytidylate deaminase zinc-binding region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9057
Polymers40,4082
Non-polymers4975
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-30 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.186, 73.073, 109.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytidine and deoxycytidylate deaminase zinc-binding region / Guanine deaminase


Mass: 20204.107 Da / Num. of mol.: 2 / Mutation: N66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298) (bacteria)
Gene: NE0047 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q82Y41
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AZG / 5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL / 8-AZAGUANINE


Mass: 152.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N6O / Feature type: SUBJECT OF INVESTIGATION / Comment: antineoplastic*YM
#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.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.19 % / Description: Flat plate-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.225 M MgCl2, 25% PEG 3350 and 0.1M BIS-TRIS, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→60.86 Å / Num. obs: 26490 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.932 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Net I/σ(I): 25.8
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.484 / Num. unique obs: 1290 / CC1/2: 0.932 / Rpim(I) all: 0.22 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HRQ

4hrq


Resolution: 1.86→60.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.065 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1260 5 %RANDOM
Rwork0.1649 ---
obs0.16748 24122 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.684 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.86→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 28 91 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192734
X-RAY DIFFRACTIONr_bond_other_d0.0020.022607
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9823732
X-RAY DIFFRACTIONr_angle_other_deg1.05435962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52223.495103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31415395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3041521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213175
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02594
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_it1.7661.9141474
X-RAY DIFFRACTIONr_mcbond_other1.7591.9121473
X-RAY DIFFRACTIONr_mcangle_it2.5412.8571840
X-RAY DIFFRACTIONr_mcangle_other2.5412.8591841
X-RAY DIFFRACTIONr_scbond_it2.7022.2271260
X-RAY DIFFRACTIONr_scbond_other2.7012.2271260
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0123.2281891
X-RAY DIFFRACTIONr_long_range_B_refined5.30615.983098
X-RAY DIFFRACTIONr_long_range_B_other5.27815.9533092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 90 -
Rwork0.195 1370 -
obs--75.22 %

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