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Yorodumi- PDB-3p69: Crystal structure of a putative secreted protein (BF4250) from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p69 | ||||||
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Title | Crystal structure of a putative secreted protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / CARBOHYDRATE METABOLISM / PUTATIVE GLYCOSIDE HYDROLASE / IG-LIKE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Immunoglobulin-like - #4120 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / Lipoprotein Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 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 | 3p69.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p69.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p69_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 3p69_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 3p69_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3p69_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/3p69 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/3p69 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 14598.162 Da / Num. of mol.: 2 / Fragment: sequence database residues 27-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF4250 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L7M9 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 27-159) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 27-159) 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: 4.01 Å3/Da / Density % sol: 69.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.7510M ammonium sulfate, 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: BL9-2 / Wavelength: 0.97898,0.97922,0.91837,0.97881 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→29.914 Å / Num. all: 29482 / Num. obs: 29482 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 40.336 Å2 / Rsym value: 0.089 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.013 / 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: 2.05→29.914 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9409 / 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 REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. GLYCEROL (GOL), USED AS A CRYOPROTECTANT AND CHLORIDE (CL) FROM THE PROTEIN BUFFER HAVE BEEN MODELED INTO THE STRUCTURE.
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Displacement parameters | Biso max: 130.59 Å2 / Biso mean: 50.6401 Å2 / Biso min: 19.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.914 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 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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