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Yorodumi- PDB-2vr5: Crystal structure of Trex from Sulfolobus Solfataricus in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vr5 | ||||||
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Title | Crystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose intermediate and glucose | ||||||
Components | GLYCOGEN OPERON PROTEIN GLGX | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / GLYCOSYL HYDROLASE | ||||||
Function / homology | Function and homology information glycogen debranching enzyme activity / glycogen catabolic process / aminopeptidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Song, H.-N. / Yoon, S.-M. / Lee, S.-J. / Cha, H.-J. / Park, K.-H. / Woo, E.-J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus. Authors: Woo, E. / Lee, S. / Cha, H. / Park, J. / Yoon, S. / Song, H. / Park, K. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vr5.cif.gz | 309.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vr5.ent.gz | 251 KB | Display | PDB format |
PDBx/mmJSON format | 2vr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vr5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2vr5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2vr5_validation.xml.gz | 69.4 KB | Display | |
Data in CIF | 2vr5_validation.cif.gz | 91.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vr5 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vr5 | HTTPS FTP |
-Related structure data
Related structure data | 2vncSC 2vuyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 6 molecules AB
#1: Protein | Mass: 83181.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DISULFIDE BOND BETWEEN A 254 AND A 261, A 505 AND A 519, B 254 AND B 261, B 505 AND B 519 Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P95868, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Sugar | ChemComp-GLC / |
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-Non-polymers , 4 types, 405 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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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: 3.26 Å3/Da / Density % sol: 62.33 % / Description: NONE |
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Crystal grow | pH: 8 Details: PEG 3K 8%, 0.2M LITHIUM SULFATE, 0.1M PH 8.0 IMIDAZOLE BUFFER |
-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 51526 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 3.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.7 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 2VNC Resolution: 2.8→29.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 48122.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.557 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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