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Yorodumi- PDB-7vxt: Crystal structure of a selenomethionine-labeled BPSL1038 from Bur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vxt | |||||||||||||||
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Title | Crystal structure of a selenomethionine-labeled BPSL1038 from Burkholderia pseudomallei | |||||||||||||||
Components | BPSL1038 | |||||||||||||||
Keywords | HYDROLASE / Nuclease / Cas2 / DSST motif | |||||||||||||||
Function / homology | BETA-MERCAPTOETHANOL / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Burkholderia pseudomallei K96243 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å | |||||||||||||||
Authors | Shaibullah, S. / Mohd-Sharif, M. / Ho, K.L. / Firdaus-Raih, M. / Nathan, S. / Mohamed, R. / Teh, A.K. / Waterman, J. / Ng, C.L. | |||||||||||||||
Funding support | Malaysia, 4items
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Citation | Journal: Commun Biol / Year: 2023 Title: Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family. Authors: Shaibullah, S. / Shuhaimi, N. / Ker, D.S. / Mohd-Sharif, N. / Ho, K.L. / Teh, A.H. / Waterman, J. / Tang, T.H. / Wong, R.R. / Nathan, S. / Mohamed, R. / Ng, M.J. / Fung, S.Y. / Jonet, M.A. / ...Authors: Shaibullah, S. / Shuhaimi, N. / Ker, D.S. / Mohd-Sharif, N. / Ho, K.L. / Teh, A.H. / Waterman, J. / Tang, T.H. / Wong, R.R. / Nathan, S. / Mohamed, R. / Ng, M.J. / Fung, S.Y. / Jonet, M.A. / Firdaus-Raih, M. / Ng, C.L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vxt.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vxt.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vxt_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
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Full document | 7vxt_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 7vxt_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7vxt_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/7vxt ftp://data.pdbj.org/pub/pdb/validation_reports/vx/7vxt | HTTPS FTP |
-Related structure data
Related structure data | 7vxrC 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 domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 2 - 86 / Label seq-ID: 22 - 106
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-Components
#1: Protein | Mass: 12306.942 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria) Strain: K96243 / Gene: BPSL1038 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q63W52 #2: Chemical | ChemComp-BME / #3: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97972 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97972 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→28.97 Å / Num. obs: 19376 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Rsym value: 0.104 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1140 / CC1/2: 0.826 / Rpim(I) all: 0.312 / Rrim(I) all: 0.72 / Rsym value: 0.645 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.88→28.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.974 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.66 Å2 / Biso mean: 32.851 Å2 / Biso min: 15.32 Å2
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Refinement step | Cycle: final / Resolution: 1.88→28.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4136 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.88→1.928 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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