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Yorodumi- PDB-3pet: Crystal structure of a putative adhesin (BF0245) from Bacteroides... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pet | ||||||
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Title | Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution | ||||||
Components | Putative adhesin | ||||||
Keywords | CELL ADHESION / RIGHT-HANDED BETA-HELIX / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Pectate Lyase C-like - #120 / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / ACETATE ION / Putative lipoprotein Function and homology information | ||||||
Biological species | Bacteroides fragilis NCTC 9343 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 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 | 3pet.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pet.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/3pet ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pet | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23451.369 Da / Num. of mol.: 2 / Fragment: sequence database residues 25-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria) Strain: ATCC 25285 / NCTC 9343 / Gene: BF0202 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LIP7 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 25-244) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-244) WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.07→45.392 Å / Num. obs: 30470 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.558 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.85 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.07→45.392 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.3 / 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. CHLORIDE (CL), ACETATE (ACT), POLYETHYLENE GLYCOL FRAGMENTS (PG4) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 3. NON-CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED DURING REFINEMENT (AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. REFINEMENT WAS RESTRAINED TO THE MAD PHASES
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Displacement parameters | Biso max: 106.68 Å2 / Biso mean: 28.836 Å2 / Biso min: 11.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→45.392 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.14 Å / Total num. of bins used: 15
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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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