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Yorodumi- PDB-7e6f: Crystal structure of PMP-bound form of cysteine desulfurase SufS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e6f | ||||||
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Title | Crystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in L-cycloserine-inhibition | ||||||
Components | Cysteine desulfurase SufS | ||||||
Keywords | BIOSYNTHETIC PROTEIN / cysteine desulfurase / PLP-dependent enzyme / cysteine metabolism / cycloserine / inhibitor / Fe-S cluster biosynthesis | ||||||
Function / homology | Function and homology information cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Nakamura, R. / Takahashi, Y. / Fujishiro, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2022 Title: Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Authors: Nakamura, R. / Ogawa, S. / Takahashi, Y. / Fujishiro, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e6f.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e6f.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 7e6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/7e6f ftp://data.pdbj.org/pub/pdb/validation_reports/e6/7e6f | HTTPS FTP |
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-Related structure data
Related structure data | 6kfyC 7ceoC 7cepC 7ceqC 7cerC 7cesC 7cetC 7ceuC 7e6aC 7e6bC 7e6cC 7e6dC 7e6eC 5zs9S 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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-Components
#1: Protein | Mass: 46500.465 Da / Num. of mol.: 1 / Mutation: R376A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-PMP / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.74→46.44 Å / Num. obs: 17471 / % possible obs: 99.9 % / Redundancy: 20.225 % / Biso Wilson estimate: 75.225 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.113 / Χ2: 0.86 / Net I/σ(I): 19.74 / Num. measured all: 353349 / Scaling rejects: 23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZS9 Resolution: 2.74→46.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.613 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 173.62 Å2 / Biso mean: 75.465 Å2 / Biso min: 39.18 Å2
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Refinement step | Cycle: final / Resolution: 2.74→46.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.811 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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