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Yorodumi- PDB-3nmb: Crystal structure of a putative sugar hydrolase (BACOVA_03189) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nmb | ||||||
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Title | Crystal structure of a putative sugar hydrolase (BACOVA_03189) from Bacteroides ovatus at 2.40 A resolution | ||||||
Components | putative sugar hydrolase | ||||||
Keywords | HYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | 3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Exo-inulinase; domain 1 / Jelly Rolls / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / DUF1080 domain-containing protein Function and homology information | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative sugar hydrolase (BACOVA_03189) from Bacteroides ovatus at 2.40 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 | 3nmb.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nmb.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nmb ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nmb | 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 29354.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03189 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LZB4 | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 30-288) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 30-288) 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: 4.02 Å3/Da / Density % sol: 69.43 % Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1 Details: 0.200M Na2HPO4, 20.00% PEG-3350, No Buffer, pH 9.1, 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: 0.91837,0.97931,0.97868 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.4→28.825 Å / Num. obs: 18955 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.298 Å2 / Rmerge(I) obs: 0.195 / Net I/σ(I): 6.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.4→28.825 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.169 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.191 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 U 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 U 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. 7. POLYETHYLENE GLYCOL-3350 (PEG) FRAGMENTS AND ETHYLENE GLYCOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION AND A SODIUM ION (NA) FROM THE PROTEIN BUFFER ARE MODELED.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.28 Å2 / Biso mean: 48.7775 Å2 / Biso min: 34.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→28.825 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.952 Å / Origin y: 41.673 Å / Origin z: 36.928 Å
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