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Yorodumi- PDB-3sd2: Crystal structure of a putative member of duf3244 protein family ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sd2 | ||||||
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Title | Crystal structure of a putative member of duf3244 protein family (BT_3571) from Bacteroides thetaiotaomicron vpi-5482 at 1.40 A resolution | ||||||
Components | Putative member of DUF3244 protein family | ||||||
Keywords | UNKNOWN FUNCTION / Immunoglobulin-like beta-sandwich / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Immunoglobulin-like - #3080 / Protein of unknown function DUF3244 / Domain of unknown function (DUF3244) / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Putative member of DUF3244 protein family (BT_3571) from Bacteroides thetaiotaomicron VPI-5482 at 1.40 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 | 3sd2.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sd2.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/3sd2 ftp://data.pdbj.org/pub/pdb/validation_reports/sd/3sd2 | HTTPS FTP |
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-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: 11282.390 Da / Num. of mol.: 1 / Fragment: sequence database residues 19-118 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_3571 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A1T7 |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT (RESIDUES 19-118) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 19-118) 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: 2.38 Å3/Da / Density % sol: 48.24 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 | Details: 30.00% polyethylene glycol 200, 1.00M lithium sulfate, 0.1M sodium citrate pH 5.6, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97935,0.97898 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→29.325 Å / Num. obs: 21813 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.649 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.97 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4→29.325 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.812 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.059 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. THE SIDECHAIN OF CYS A109 SHOWS MULTIPLE CONFORMATIONS. IT WAS MODELED WITH A DISULFIDE BOND BETWEEN CONFORMER A AND THE SYMMETRY RELATED CONFORMER A. CONFORMERS B AND C WERE MODELED AS NOT FORMING A DISULFIDE BOND TO SYMMETRY RELATED ATOMS.
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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: 65.97 Å2 / Biso mean: 21.8402 Å2 / Biso min: 11.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.325 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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