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Yorodumi- PDB-3nnb: Crystal structure of an alginate lyase (BACOVA_01668) from Bacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nnb | ||||||
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Title | Crystal structure of an alginate lyase (BACOVA_01668) from Bacteroides ovatus at 1.60 A resolution | ||||||
Components | alginate lyase | ||||||
Keywords | LYASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of an alginate lyase (BACOVA_01668) from Bacteroides ovatus at 1.60 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 | 3nnb.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nnb.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nnb_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 3nnb_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 3nnb_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3nnb_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/3nnb ftp://data.pdbj.org/pub/pdb/validation_reports/nn/3nnb | 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
#1: Protein | Mass: 44051.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_01668 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LV19 | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 20-400) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-400) 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: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.600000000M NaCitrate, No Buffer pH 6.5, 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: 0.9787 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.137 Å / Num. obs: 60601 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.658 Å2 / Rsym value: 0.126 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→29.137 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.307 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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. CITRATE (CIT), SODIUM (NA) AND GLYCEROL (GOL) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.61 Å2 / Biso mean: 14.63 Å2 / Biso min: 3.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.137 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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