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

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Basic information

Entry
Database: PDB / ID: 7dow
TitleThe structure of the Arabidopsis thaliana guanosine deaminase in reaction with 7-deazaguansoine
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-HD3 / Guanosine deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,7416
Polymers35,0462
Non-polymers6954
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-30 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.075, 119.075, 39.692
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-HD3 / 2-azanyl-7-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3H-pyrrolo[2,3-d]pyrimidin-4-one


Mass: 282.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O5 / 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.: 273 / 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: 46.93 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→23.66 Å / Num. obs: 21954 / % possible obs: 98.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 16.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3095 / CC1/2: 0.841 / % possible all: 94.8

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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: 2→23.66 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9577 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 1054 4.8 %
Rwork0.1685 20887 -
obs0.1703 21941 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.09 Å2
Refinement stepCycle: LAST / Resolution: 2→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 42 273 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322462
X-RAY DIFFRACTIONf_angle_d0.5793331
X-RAY DIFFRACTIONf_chiral_restr0.0424372
X-RAY DIFFRACTIONf_plane_restr0.004431
X-RAY DIFFRACTIONf_dihedral_angle_d5.37531451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.30061170.21282536X-RAY DIFFRACTION97.04
2.09-2.20.23481120.18242615X-RAY DIFFRACTION99.16
2.2-2.340.22811420.17392575X-RAY DIFFRACTION99.78
2.34-2.520.21871410.16942569X-RAY DIFFRACTION100
2.52-2.770.2221600.17462594X-RAY DIFFRACTION100
2.77-3.170.20181380.17072610X-RAY DIFFRACTION100
3.17-3.990.17851060.15462677X-RAY DIFFRACTION100
3.99-23.660.17371380.15672711X-RAY DIFFRACTION100

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