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Yorodumi- PDB-1dex: RHAMNOGALACTURONAN ACETYLESTERASE FROM ASPERGILLUS ACULEATUS AT 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dex | |||||||||
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Title | RHAMNOGALACTURONAN ACETYLESTERASE FROM ASPERGILLUS ACULEATUS AT 1.9 A RESOLUTION | |||||||||
Components | RHAMNOGALACTURONAN ACETYLESTERASE | |||||||||
Keywords | HYDROLASE / SGNH HYDROLASE | |||||||||
Function / homology | Function and homology information rhamnogalacturonan acetylesterase / hydrolase activity, acting on ester bonds Similarity search - Function | |||||||||
Biological species | Aspergillus aculeatus (mold) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | |||||||||
Authors | Molgaard, A. / Kauppinen, S. / Larsen, S. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Authors: Molgaard, A. / Kauppinen, S. / Larsen, S. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus Authors: Kauppinen, S. / Christgau, S. / Kofod, L.V. / Halkier, T. / Dorreich, K. / Dalboge, H. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary x-ray diffraction studies of the heterogeneously glycosylated enzyme rhamnogalacturonan acetylesterase from Aspergillus aculeatus Authors: Molgaard, A. / Petersen, J. / Kauppinen, S. / Dalboge, H. / Johnsen, A. / Navarro Poulsen, J.-C. / Larsen, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dex.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dex.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1dex ftp://data.pdbj.org/pub/pdb/validation_reports/de/1dex | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 24622.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus (mold) / Strain: KSM 510 / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): A1560 / References: EMBL: Q00017, UniProt: Q00017*PLUS |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.78 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG 4000, 2-propanol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 19, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 15662 / Num. obs: 15662 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.258 / Num. unique all: 1592 / % possible all: 64.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 64.1 % |
-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.162 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_d / Dev ideal: 24.5 |