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Yorodumi- PDB-3flj: Crystal structure of uncharacterized protein conserved in bacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3flj | ||||||
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Title | Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution | ||||||
Components | uncharacterized protein conserved in bacteria with a cystatin-like fold | ||||||
Keywords | structural genomics / unknown function / YP_168589.1 / uncharacterized protein conserved in bacteria with a cystatin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Unknown ligand / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | SILICIBACTER POMEROYI DSS-3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 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 | 3flj.cif.gz | 43 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3flj.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 3flj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3flj_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 3flj_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 3flj_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3flj_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/3flj ftp://data.pdbj.org/pub/pdb/validation_reports/fl/3flj | 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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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 18103.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SILICIBACTER POMEROYI DSS-3 (bacteria) / Gene: SPO3393, YP_168589.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LN19 |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT 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: 4.07 Å3/Da / Density % sol: 69.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2000M MgCl2, 2.5000M NaCl, 0.1M TRIS pH 7.0, 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: BL9-2 / Wavelength: 0.91837,0.97982 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→28.49 Å / Num. obs: 19903 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.973 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.95 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2→28.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.615 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.098 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN THE CORE OF THE PROTEIN SURROUNDED BY BOTH HYDROPHOBIC AND HYDROPHILLIC RESIDUES.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.63 Å2 / Biso mean: 48.955 Å2 / Biso min: 30.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 58.497 Å / Origin y: 24.106 Å / Origin z: 11.656 Å
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