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Yorodumi- PDB-6kzw: Crystal structure of YggS family pyridoxal phosphate-dependent en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kzw | |||||||||
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Title | Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum | |||||||||
Components | Pyridoxal phosphate homeostasis protein | |||||||||
Keywords | PROTEIN BINDING / Fusobacterium nucleatum / YggS family pyridoxal phosphate-dependent enzyme / PipY / PLP-binding protein | |||||||||
Function / homology | Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / PLP-binding barrel / pyridoxal phosphate binding / PHOSPHATE ION / Pyridoxal phosphate homeostasis protein / Pyridoxal phosphate homeostasis protein Function and homology information | |||||||||
Biological species | Fusobacterium nucleatum subsp. nucleatum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å | |||||||||
Authors | Chen, Y. / Wang, L. / Shang, F. / Lan, J. / Liu, W. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum Authors: Chen, Y. / Wang, L. / Shang, F. / Lan, J. / Liu, W. / Xu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kzw.cif.gz | 192 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kzw.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/6kzw ftp://data.pdbj.org/pub/pdb/validation_reports/kz/6kzw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26212.266 Da / Num. of mol.: 3 / Mutation: T5A, N202S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria) Gene: RO03_02185 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A117MW82, UniProt: Q8RFW9*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.63 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate 20% w/v polyethylene glycol 4,000 0.1 M Sodium acetate trihydrate(pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 47064 / % possible obs: 96.1 % / Redundancy: 6 % / Biso Wilson estimate: 24.37 Å2 / Rsym value: 0.271 / Net I/σ(I): 27.13 |
Reflection shell | Resolution: 2.08→2.12 Å / Num. unique obs: 1000 / Rsym value: 0.271 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.08→37 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.7369
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→37 Å
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Refine LS restraints |
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LS refinement shell |
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