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Yorodumi- PDB-4qni: Crystal structure of an auxiliary nutrient binding protein (BT350... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qni | ||||||
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Title | Crystal structure of an auxiliary nutrient binding protein (BT3507) from Bacteroides thetaiotaomicron VPI-5482 at 2.30 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / N-terminal- PF08522 family (DUF1735) / C-terminal - PF14274 family (DUF4361) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (BT3507) from Bacteroides thetaiotaomicron VPI-5482 at 2.30 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 | 4qni.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qni.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/4qni ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qni | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37941.039 Da / Num. of mol.: 1 / Fragment: UNP residues 22-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3507 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A201 | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (22-353) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-353) 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: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.40M tri-Sodium Citrate, 0.1M sodium HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97932,0.95369,0.97903 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 26, 2014 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→28.576 Å / Num. obs: 17102 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.333 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.71 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.3→28.576 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9355 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL (MAD) PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. CITRATE (CIT) FROM THE CRYSTALLIZATION, CHLORIDE (CL) FROM THE PURIFICATION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. RAMACHANDRAN OUTLIER AT RESIDUE 36 IS IN A REGION OF SUBOPTIMAL ELECTRON DENSITY THAT IS DIFFICULT TO MODEL.
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Displacement parameters | Biso max: 132 Å2 / Biso mean: 58.5742 Å2 / Biso min: 30.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.302 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.576 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 44.5254 Å / Origin y: 19.78 Å / Origin z: 24.4276 Å
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Refinement TLS group | Selection details: { A|29 - 353 } |