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- PDB-4ygu: Crystal structure of a putative adhesin (BACEGG_01763) from Bacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ygu | ||||||
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Title | Crystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution | ||||||
![]() | putative adhesin | ||||||
![]() | CELL ADHESION / PF10988 family protein / DUF2807 / single-strabded right handed beta-helix fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.2 KB | Display | ![]() |
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PDB format | ![]() | 220.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.5 KB | Display | ![]() |
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Full document | ![]() | 500.2 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19878.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BACEGG_01763 / Plasmid: SpeedET / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PGE / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 25-207) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 25-207) WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.67 Details: 1.0M lithium chloride, 22% polyethylene glycol 6000, 0.2M NDSB-256, 0.1M TRIS pH 8.67 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2014 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled 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: 2.2→48.579 Å / Num. obs: 40038 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.05 % / Biso Wilson estimate: 36.546 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.157 / Net I/σ(I): 9.93 / Num. measured all: 322328 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1.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: 1.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.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. MAD PHASES WERE USED AS RESTRAINTS DURING THE REFINEMENT. 5. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 6. POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 7.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAS BEEN MODELED INTO THE SOLVENT STRUCTURE.
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Displacement parameters | Biso max: 180.24 Å2 / Biso mean: 64.6273 Å2 / Biso min: 10.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.413 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.579 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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