+Open data
-Basic information
Entry | Database: PDB / ID: 3l9t | ||||||
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Title | The Crystal Structure of smu.31 from Streptococcus mutans UA159 | ||||||
Components | Putative uncharacterized protein smu.31 | ||||||
Keywords | UNKNOWN FUNCTION / hypothetical protein | ||||||
Function / homology | Function and homology information Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #70 / ARM repeat domains / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.206 Å | ||||||
Authors | Su, X.-D. / Cao, Q. / Liu, X. | ||||||
Citation | Journal: TO BE PUBLISHED Title: The Crystal Structure of smu.31 from Streptococcus mutans UA159 Authors: Su, X.-D. / Cao, Q. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l9t.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l9t.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 3l9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l9t_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 3l9t_full_validation.pdf.gz | 439.7 KB | Display | |
Data in XML | 3l9t_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3l9t_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9t ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9t | 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: 28449.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.31 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DWL4 |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14% PEG 6000, 0.1M HEPES pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 12788 / Num. obs: 12558 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 23.98 Å2 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.206→19.569 Å / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.836 / SU ML: 0.32 / σ(F): 2.03 / Phase error: 22.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.907 Å2 / ksol: 0.454 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.01 Å2 / Biso mean: 24.455 Å2 / Biso min: 9.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.206→19.569 Å
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Refine LS restraints |
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LS refinement shell |
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