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Yorodumi- PDB-4q53: Crystal structure of a DUF4783 family protein (BACUNI_04292) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q53 | ||||||
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Title | Crystal structure of a DUF4783 family protein (BACUNI_04292) from Bacteroides uniformis ATCC 8492 at 1.27 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / DUF4783 / PF16022 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Protein of unknown function DUF4783 / Domain of unknown function (DUF4783) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.27 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (BACUNI_04292) from Bacteroides uniformis ATCC 8492 at 1.27 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 | 4q53.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q53.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q53 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q53 | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12458.679 Da / Num. of mol.: 2 / Fragment: UNP residues 22-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_04292 / Plasmid: SpeedE5T / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V9L7 |
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-Non-polymers , 8 types, 208 molecules
#2: Chemical | ChemComp-IOD / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-7PG / | #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT (RESIDUES 21-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-130) WAS EXPRESSED WITH A PURIFICATI |
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-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: 41.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.07M Sodium Iodide, 30.00% polyethylene glycol 3350, 0.01M ferric(III) chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2013 Details: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) | |||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL SI(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97882 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.27→28.002 Å / Num. obs: 53919 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.53 Å2 | |||||||||||||||
Reflection shell | Resolution: 1.27→1.32 Å / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.27→28 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.09 / Phase error: 14.2 / Stereochemistry target values: MLHL 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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. IODIDES (IOD) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. THE MODELING OF IODIDE IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS. 4. POLYETHYLENE GLYCOL FRAGMENTS (7PE,PEG, AND PG4) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 5. SODIUM (NA) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 1,2- ETHANEDIOL (EDO), USED AS A CRYOPROTECTANT, HAS ALSO BEEN MODELED INTO THE STRUCTURE. 5. HYDROGENS HAVE BEEN ADDED AT THE RIDING POSITIONS. 6. ELECTRON DENSITY INDICATES THAT CYS 109 ON THE TWO SUBUNITS IN THE ASYMMETRIC UNIT ARE OXIDIZED; THEREFORE, THESE RESIDUES WERE MODELED AS S-HYDROXYCYSTEINE (CSO).
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→28 Å
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Refine LS restraints |
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LS refinement shell |
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