+Open data
-Basic information
Entry | Database: PDB / ID: 1c0n | ||||||
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Title | CSDB PROTEIN, NIFS HOMOLOGUE | ||||||
Components | PROTEIN (CSDB PROTEIN) | ||||||
Keywords | LYASE / ALPHA/BETA FOLD | ||||||
Function / homology | Function and homology information selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Fujii, T. / Maeda, M. / Mihara, H. / Kurihara, T. / Esaki, N. / Hata, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase Authors: Fujii, T. / Maeda, M. / Mihara, H. / Kurihara, T. / Esaki, N. / Hata, Y. #1: Journal: J.Biol.Chem. / Year: 1999 Title: A nifS-like Gene, csdB, Encodes an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase. GENE CLONING, PURIFICATION, CHARACTERIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDIES Authors: Mihara, H. / Maeda, M. / Fujii, T. / Kurihara, T. / Hata, Y. / Esaki, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c0n.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c0n.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c0n_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 1c0n_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 1c0n_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1c0n_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c0n ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c0n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44077.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCSDB / Production host: Escherichia coli (E. coli) / References: UniProt: P77444 |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-ACY / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: sodium acetate, pottasium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 62 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→93.6 Å / Num. all: 27061 / Num. obs: 27061 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 2.8→3 Å / Rmerge(I) obs: 0.216 / Num. unique all: 4641 / % possible all: 88.5 |
Reflection | *PLUS Num. obs: 23770 / Num. measured all: 73138 |
Reflection shell | *PLUS % possible obs: 88.5 % |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.29 / Num. reflection obs: 2000 |