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Yorodumi- PDB-4j8q: Crystal structure of a NigD-like protein (BF0700) from Bacteroide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j8q | ||||||
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Title | Crystal structure of a NigD-like protein (BF0700) from Bacteroides fragilis NCTC 9343 at 2.50 A resolution | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NigD-like protein / PF12667 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Prokaryotic membrane lipoprotein lipid attachment site profile. ...NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (BF0700) from Bacteroides fragilis NCTC 9343 at 2.50 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 | 4j8q.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j8q.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 4j8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j8q_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 4j8q_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 4j8q_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4j8q_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8q ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8q | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 25692.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF0700, BF9343_0666 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5LHD5 |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT 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: 2.7 Å3/Da / Density % sol: 54.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium nitrate, 20% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97944,0.97853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal 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: 2.5→28.767 Å / Num. obs: 9419 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.5→28.767 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 17.376 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.275 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTION SOLUTION IS MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.77 Å2 / Biso mean: 44.2726 Å2 / Biso min: 17.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→28.767 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.568 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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