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Open data
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Basic information
Entry | Database: PDB / ID: 7ww2 | ||||||
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Title | Structure of an Isocytosine specific deaminase Vcz | ||||||
![]() | 8-oxoguanine deaminase | ||||||
![]() | HYDROLASE / deaminase / isocytosine / cancer therapy / 5-fluorouracil | ||||||
Function / homology | 8-oxoguanine deaminase activity / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Hydroxydechloroatrazine ethylaminohydrolase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X.J. / Wu, B.X. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy. Authors: Guo, W. / Li, X. / Fan, J. / Li, H. / Wen, Y. / Meng, C. / Chen, H. / Zhao, Z. / Zhang, Y. / Du, Y. / Wu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 418.4 KB | Display | ![]() |
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PDB format | ![]() | 284.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8is4C ![]() 8is5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.994547817682, -0.103989117524, -0.00780395933365), (-0.10421398802, 0.988423534813, 0.110264956034), (-0.00375273840167, 0.110477053115, -0.993871590141)Vector: -5. ...NCS oper: (Code: given Matrix: (-0.994547817682, -0.103989117524, -0.00780395933365), Vector: |
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Components
#1: Protein | Mass: 49544.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 25076 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 3613 / CC1/2: 0.963 / Rpim(I) all: 0.214 / Rrim(I) all: 0.576 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.71006930743 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.96421506634 Å / Origin y: -15.8795070429 Å / Origin z: -28.2430535083 Å
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Refinement TLS group | Selection details: all |