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Yorodumi- PDB-3ejn: CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BF3025) FROM BACTEROIDES FRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ejn | ||||||
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Title | CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BF3025) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.50 A RESOLUTION | ||||||
Components | SusD homolog | ||||||
Keywords | SUGAR BINDING PROTEIN / SUSD HOMOLOG / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information SusD-like, tetratrico peptide repeats domain / SusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacteroides fragilis NCTC 9343 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of SusD homolog (YP_212639.1) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ejn.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ejn.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ejn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ejn_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 3ejn_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 3ejn_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3ejn_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/3ejn ftp://data.pdbj.org/pub/pdb/validation_reports/ej/3ejn | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54931.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria) Gene: YP_212639.1, BF3025 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LB02, UniProt: A0A380YV80*PLUS | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 18-490) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 18-490) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M magnesium formate, 18.5% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97876,0.97822 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→29.074 Å / Num. obs: 81072 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.439 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 17.05 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→29.074 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 2.624 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. MG, FMT, AND PG4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 3. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. MG, FMT, AND PG4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 3. THE DATASET IS TWINNED WITH THE OPERATOR "-H-K, K, -L". THE FINAL REFINED TWIN FRACTION IS 0.3235
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.07 Å2 / Biso mean: 22.997 Å2 / Biso min: 7.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.074 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.499→1.538 Å / Total num. of bins used: 20
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