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- PDB-7dpk: The structure of the exchange reaction of the Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 7dpk
TitleThe structure of the exchange reaction of the Arabidopsis thaliana guanosine deaminase in complex with 7-deazaguaosine by guanosine
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 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine Deaminase; domain 2 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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 19, 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)35,4615
Polymers35,0462
Non-polymers4153
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-65 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.027, 119.027, 38.919
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-4UO / 2,3-dihydroxanthosine / Xanthosine


Mass: 284.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O6 / 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.: 179 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
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: Sep 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→23.65 Å / Num. obs: 17452 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Net I/σ(I): 18
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2513 / CC1/2: 0.905 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DBF

7dbf


Resolution: 2.15→23.65 Å / SU ML: 0.193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1717 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 893 5.12 %
Rwork0.172 16543 -
obs0.1736 17436 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.94 Å2
Refinement stepCycle: LAST / Resolution: 2.15→23.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 22 179 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282456
X-RAY DIFFRACTIONf_angle_d0.53223319
X-RAY DIFFRACTIONf_chiral_restr0.0416369
X-RAY DIFFRACTIONf_plane_restr0.0037433
X-RAY DIFFRACTIONf_dihedral_angle_d5.02181738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.280.24651640.19562720X-RAY DIFFRACTION100
2.28-2.460.20971250.18272726X-RAY DIFFRACTION100
2.46-2.710.22731470.18482742X-RAY DIFFRACTION99.97
2.71-3.10.17521720.17232714X-RAY DIFFRACTION100
3.1-3.90.19411340.15442801X-RAY DIFFRACTION100
3.9-23.650.19511510.16822840X-RAY DIFFRACTION99.93

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