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Yorodumi- PDB-3on6: Crystal structure of an exo-alpha-1,6-mannosidase (bacova_03626) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3on6 | ||||||
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Title | Crystal structure of an exo-alpha-1,6-mannosidase (bacova_03626) from bacteroides ovatus at 1.70 a resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / ALPHA/ALPHA TOROID FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Bacterial protein of unknown function (BACOVA_03626) from Bacteroides ovatus at 1.70 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 | 3on6.cif.gz | 380.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3on6.ent.gz | 310.6 KB | Display | PDB format |
PDBx/mmJSON format | 3on6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3on6 ftp://data.pdbj.org/pub/pdb/validation_reports/on/3on6 | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A POSSIBLE OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 53459.109 Da / Num. of mol.: 2 / Fragment: sequence database residues 22-481 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_03626 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M0J6 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.18 Å3/Da / Density % sol: 43.54 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 | Details: 1.00M LiCl, 20.00% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97944,0.97886 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→29.044 Å / Num. obs: 100307 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.103 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.7→29.044 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.119 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 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. CHLORIDE (CL) AND POLYETHYLENE GLYCROL (PEG) FROM THE CRYSTALLIZATION AND ETHYLENE GLYCOL(EDO) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.66 Å2 / Biso mean: 11.8343 Å2 / Biso min: 3.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.044 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6032 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 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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