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Yorodumi- PDB-5b55: Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b55 | |||||||||
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Title | Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form | |||||||||
Components | Cysteine synthase | |||||||||
Keywords | TRANSFERASE / Pyridoxal 5'-phosphate dependent enzyme / alpha-Aminoacrylate | |||||||||
Function / homology | Function and homology information cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm Similarity search - Function | |||||||||
Biological species | Fusobacterium nucleatum subsp. nucleatum strain ATCC 25586 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | |||||||||
Authors | Kezuka, Y. / Yoshida, Y. / Nonaka, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochem. J. / Year: 2018 Title: Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,Fusobacterium nucleatum. Authors: Kezuka, Y. / Ishida, T. / Yoshida, Y. / Nonaka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b55.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b55.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5b55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b55 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b55 | HTTPS FTP |
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-Related structure data
Related structure data | 5z5cC 5b53S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 3 - 334 / Label seq-ID: 7 - 338
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-Components
#1: Protein | Mass: 38564.113 Da / Num. of mol.: 2 / Mutation: D232N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum strain ATCC 25586 (bacteria) Strain: ATCC 25586 / Gene: FN1055 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8REP3, cysteine synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.3 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% (w/v) PEG3350, 0.1M Hepes pH 7.5, 0.2M Magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→60.43 Å / Num. obs: 52807 / % possible obs: 95.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7.3 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B53 Resolution: 2.14→36.66 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.445 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 24.482 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→36.66 Å
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Refine LS restraints |
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