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

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Basic information

Entry
Database: PDB / ID: 7doy
TitleThe structure of the Arabidopsis thaliana guanosine deaminase in complex with 6-O-methylguanosine
ComponentsGuanosine deaminase
KeywordsPLANT PROTEIN / 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
Chem-HD9 / Guanosine deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsXie, W. / Jia, Q. / Zeng, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: To Be Published
Title: Asymmetric Catalysis of Arabidopsis thaliana Guanosine Deaminase Revealed by Crystal Structures
Authors: Xie, W. / Jia, Q. / Zeng, H.
History
DepositionDec 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,7716
Polymers35,0462
Non-polymers7254
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-29 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.130, 119.130, 39.733
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-HD9 / (2R,3R,4S,5R)-2-(2-azanyl-6-methoxy-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol


Mass: 297.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O5 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2 M Na-citrate and 0.1 M 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: 2.17→50 Å / Num. obs: 17386 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.18 / Net I/σ(I): 25.6
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 6.333 / Num. unique obs: 1711 / CC1/2: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DBF

7dbf


Resolution: 2.17→28.61 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8036 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 881 5.08 %
Rwork0.173 16469 -
obs0.175 17350 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.7 Å2
Refinement stepCycle: LAST / Resolution: 2.17→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 44 152 2562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252454
X-RAY DIFFRACTIONf_angle_d0.55863321
X-RAY DIFFRACTIONf_chiral_restr0.0413372
X-RAY DIFFRACTIONf_plane_restr0.0036429
X-RAY DIFFRACTIONf_dihedral_angle_d5.81381445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.310.25711490.18662697X-RAY DIFFRACTION99.72
2.31-2.480.24191270.18822766X-RAY DIFFRACTION99.93
2.48-2.730.25141520.19272684X-RAY DIFFRACTION99.96
2.73-3.130.2361720.19922722X-RAY DIFFRACTION100
3.13-3.940.20191320.16222768X-RAY DIFFRACTION100
3.94-28.610.17821490.15682832X-RAY DIFFRACTION99.8

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