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- PDB-7c3t: Crystal structure of NE0047 (N66Q) mutant in complex with 8-azaguanine -

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Basic information

Entry
Database: PDB / ID: 7c3t
TitleCrystal structure of NE0047 (N66Q) mutant in complex with 8-azaguanine
ComponentsCytidine and deoxycytidylate deaminase zinc-binding region
KeywordsHYDROLASE / DEAMINASE / 8-AZAGUANINE / COMPLEX
Function / homology
Function and homology information


hydrolase activity / 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: 2.07 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 23, 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)41,3486
Polymers40,9132
Non-polymers4354
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-32 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.168, 73.827, 110.263
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: 20456.357 Da / Num. of mol.: 2 / Mutation: N66Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 35.21 % / Description: Flat plate-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.225M MgCl2, 25% PEG 3350, 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: 2.07→61.3 Å / Num. obs: 19828 / % possible obs: 99.3 % / Redundancy: 5.37 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.045 / Rrim(I) all: 0.106 / Net I/σ(I): 15.1
Reflection shellResolution: 2.07→2.11 Å / Rmerge(I) obs: 0.472 / Num. unique obs: 935 / Rpim(I) all: 0.234 / % possible all: 95.9

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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: 2.07→61.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.132 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 957 5.1 %RANDOM
Rwork0.17864 ---
obs0.18176 17682 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.07→61.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 24 47 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192751
X-RAY DIFFRACTIONr_bond_other_d0.0020.022611
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9773755
X-RAY DIFFRACTIONr_angle_other_deg1.05135967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26723.458107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1615397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1581522
X-RAY DIFFRACTIONr_chiral_restr0.0990.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02607
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_it1.8942.4921480
X-RAY DIFFRACTIONr_mcbond_other1.8842.4891479
X-RAY DIFFRACTIONr_mcangle_it2.6613.7221847
X-RAY DIFFRACTIONr_mcangle_other2.6653.7251848
X-RAY DIFFRACTIONr_scbond_it2.5992.8071271
X-RAY DIFFRACTIONr_scbond_other2.5822.8051269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8254.1011907
X-RAY DIFFRACTIONr_long_range_B_refined5.06420.5763081
X-RAY DIFFRACTIONr_long_range_B_other5.0520.5733079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 51 -
Rwork0.211 1063 -
obs--76.56 %

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