+Open data
-Basic information
Entry | Database: PDB / ID: 7xel | ||||||
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Title | SufS soaked with D-penicillamine | ||||||
Components | Cysteine desulfurase SufS | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Cysteine desulfurase / Inhibitor | ||||||
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: 1.8 Å | ||||||
Authors | Nakamura, R. / Fujishiro, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: to be published Title: X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine Authors: Nakamura, R. / 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 | 7xel.cif.gz | 183.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xel.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 7xel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xel_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 7xel_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 7xel_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7xel_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/7xel ftp://data.pdbj.org/pub/pdb/validation_reports/xe/7xel | HTTPS FTP |
-Related structure data
Related structure data | 7xejC 7xekC 7xenC 7xeqC 7xesC 5zs9S S: Starting model for refinement 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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-Components
#1: Protein | Mass: 46814.699 Da / Num. of mol.: 1 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) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | #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: 3.44 Å3/Da / Density % sol: 64.24 % |
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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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.5 Å / Num. obs: 60337 / % possible obs: 100 % / Redundancy: 7.373 % / Biso Wilson estimate: 46.951 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.036 / Χ2: 0.922 / Net I/σ(I): 25.54 / Num. measured all: 444887 / Scaling rejects: 58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→46.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.835 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / 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: 121.64 Å2 / Biso mean: 46.637 Å2 / Biso min: 27.24 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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