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Yorodumi- PDB-5b87: Crystal structure of a Cysteine Desulfurase from Thermococcus onn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b87 | ||||||
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Title | Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 2.3 Angstrom resolution | ||||||
Components | Cysteine desulfurase | ||||||
Keywords | TRANSFERASE / Cysteine desulfurase / Cysteine Trasferases | ||||||
Function / homology | Function and homology information cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Thermococcus onnurineus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Ho, T.-H. / Kang, L.-W. | ||||||
Citation | Journal: Archaea / Year: 2017 Title: Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the ArchaeonThermococcus onnurineus NA1. Authors: Ho, T.-H. / Huynh, K.-H. / Nguyen, D.Q. / Park, H. / Jung, K. / Sur, B. / Ahn, Y.-J. / Cha, S.-S. / Kang, L.-W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b87.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b87.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b87_validation.pdf.gz | 489.7 KB | Display | wwPDB validaton report |
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Full document | 5b87_full_validation.pdf.gz | 508.5 KB | Display | |
Data in XML | 5b87_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5b87_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/5b87 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/5b87 | HTTPS FTP |
-Related structure data
Related structure data | 5b7sSC 5b7uC 5b89C 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: 46704.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea) Strain: NA1 / Gene: TON_0289 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6YT87, cysteine desulfurase #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 5mM L-alanine, 1mM PLP and 0.1 M Tris (base)/ Bicine pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 40955 / % possible obs: 95.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.28→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B7S Resolution: 2.28→49.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.143 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.222 / 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: 43.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→49.4 Å
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Refine LS restraints |
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