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Yorodumi- PDB-8is5: Structure of an Isocytosine specific deaminase Vcz with close state -
+Open data
-Basic information
Entry | Database: PDB / ID: 8is5 | ||||||
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Title | Structure of an Isocytosine specific deaminase Vcz with close state | ||||||
Components | Hydroxydechloroatrazine ethylaminohydrolase | ||||||
Keywords | HYDROLASE / isocytosine / deaminase / VCZ / 5-FU | ||||||
Function / homology | 8-oxoguanine deaminase activity / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Hydroxydechloroatrazine ethylaminohydrolase Function and homology information | ||||||
Biological species | Obesumbacterium proteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Guo, W.T. / Li, X.J. / Wu, B.X. | ||||||
Funding support | 1items
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Citation | Journal: Iscience / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8is5.cif.gz | 442.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8is5.ent.gz | 302.4 KB | Display | PDB format |
PDBx/mmJSON format | 8is5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8is5_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 8is5_full_validation.pdf.gz | 467.6 KB | Display | |
Data in XML | 8is5_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 8is5_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/8is5 ftp://data.pdbj.org/pub/pdb/validation_reports/is/8is5 | HTTPS FTP |
-Related structure data
Related structure data | 7ww2C 8is4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: givenMatrix: (-0.994020391669, -0.108734195086, -0.0100167742251), (-0.109141668904, 0.986493458874, 0.122142341991), (-0.00339956699023, 0.122505226081, -0.992462045887)Vector: -5. ...NCS oper: (Code: given Matrix: (-0.994020391669, -0.108734195086, -0.0100167742251), Vector: |
-Components
#1: Protein | Mass: 49544.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Obesumbacterium proteus (bacteria) / Gene: DSM2777_13610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q9D6T1 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 Lithium sulfate monohydrate, 0.1 M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 53026 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 33.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3 / Num. unique obs: 7634 / CC1/2: 0.857 / Rpim(I) all: 0.275 / Rrim(I) all: 1.014 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.83 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8713 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.974234491845 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.1586790456 Å / Origin y: -15.7819950985 Å / Origin z: -28.1846790267 Å
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Refinement TLS group | Selection details: all |