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- PDB-7dh1: The structure of the Arabidopsis thaliana guanosine deaminase in ... -

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Basic information

Entry
Database: PDB / ID: 7dh1
TitleThe structure of the Arabidopsis thaliana guanosine deaminase in reaction with N2-Methylguanosine
ComponentsGuanosine deaminase
KeywordsHYDROLASE / deamination / GSDA / purine metabolism
Function / homology
Function and homology information


guanosine deaminase / guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-dihydroxanthosine / Guanosine deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXie, W. / Jia, Q. / Zeng, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies.
Authors: Jia, Q. / Zhang, J. / Zeng, H. / Tang, J. / Xiao, N. / Gao, S. / Li, H. / Xie, W.
History
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanosine deaminase
D: Guanosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7456
Polymers35,0462
Non-polymers6994
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.776, 118.776, 39.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Guanosine deaminase / tRNA-specific adenosine deaminase TAD4 / AtTAD4


Mass: 17523.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSDA, TAD4, At5g28050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94BU8, guanosine deaminase
#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-4UO / 2,3-dihydroxanthosine / Xanthosine


Mass: 284.225 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2M Na-citrate and 0.1M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 27608 / % possible obs: 99.6 % / Redundancy: 19.3 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Net I/σ(I): 28
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 2600 / CC1/2: 0.893 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DBF

7dbf


Resolution: 1.85→31.35 Å / SU ML: 0.1645 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.3105 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 1333 4.86 %
Rwork0.1633 26117 -
obs0.165 27450 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 42 196 2616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442464
X-RAY DIFFRACTIONf_angle_d1.25153332
X-RAY DIFFRACTIONf_chiral_restr0.0779372
X-RAY DIFFRACTIONf_plane_restr0.0086430
X-RAY DIFFRACTIONf_dihedral_angle_d5.84281454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.28311580.23582437X-RAY DIFFRACTION95.37
1.92-1.990.23941360.21552599X-RAY DIFFRACTION99.93
1.99-2.080.25241270.18742644X-RAY DIFFRACTION100
2.08-2.190.19271250.16742582X-RAY DIFFRACTION100
2.19-2.330.21911120.16172661X-RAY DIFFRACTION100
2.33-2.510.24571400.17032576X-RAY DIFFRACTION99.96
2.51-2.760.221210.17832627X-RAY DIFFRACTION100
2.76-3.160.20271500.17572607X-RAY DIFFRACTION100
3.16-3.980.17561360.14682660X-RAY DIFFRACTION100
3.98-31.350.16381280.14472724X-RAY DIFFRACTION99.65

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