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Yorodumi- PDB-5v1t: Crystal structure of Streptococcus suis SuiB bound to precursor p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v1t | ||||||
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Title | Crystal structure of Streptococcus suis SuiB bound to precursor peptide SuiA | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Radical SAM enzyme / Lys-Trp crosslink / Streptococcus suis / metalloenzyme / SPASM domain / RRE domain | ||||||
Function / homology | Function and homology information heme biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus suis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Davis, K.M. / Bacik, J.P. / Ando, N. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Authors: Davis, K.M. / Schramma, K.R. / Hansen, W.A. / Bacik, J.P. / Khare, S.D. / Seyedsayamdost, M.R. / Ando, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v1t.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v1t.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 5v1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v1t_validation.pdf.gz | 764.1 KB | Display | wwPDB validaton report |
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Full document | 5v1t_full_validation.pdf.gz | 764.5 KB | Display | |
Data in XML | 5v1t_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 5v1t_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/5v1t ftp://data.pdbj.org/pub/pdb/validation_reports/v1/5v1t | HTTPS FTP |
-Related structure data
Related structure data | 5v1qSC 5v1sC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 53044.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: ERS132399_01508 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Z8EWX1 |
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#2: Protein/peptide | Mass: 2436.802 Da / Num. of mol.: 1 / Fragment: UNP residues 1-22 / Source method: obtained synthetically / Source: (synth.) Streptococcus suis (bacteria) |
-Non-polymers , 4 types, 288 molecules
#3: Chemical | #4: Chemical | ChemComp-MET / | #5: Chemical | ChemComp-SAM / | #6: 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: 1.95 Å3/Da / Density % sol: 37.04 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: A solution containing 23 mg/mL of His6-tagged SuiB in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed with a stock solution of SuiA in storage ...Details: A solution containing 23 mg/mL of His6-tagged SuiB in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed with a stock solution of SuiA in storage buffer lacking DTT, yielding a final SuiA concentration of 1.9 mM. The resultant solution was incubated for 10 min after which it was combined 1:1 with precipitant solution to form a 4 uL drop. Crystals appeared within 2 days and were fully grown within a week. The precipitant solution was generated by combining 100 mM Bis-Tris, pH 6.0, 200 mM Li2SO4, 27% (w/v) PEG 3350 with 210 mM SAM in water to yield a final SAM concentration of 10.5 mM. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.24 Å / Num. obs: 25903 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2044 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V1Q Resolution: 2.1→29.235 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.235 Å
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Refine LS restraints |
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LS refinement shell |
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