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Yorodumi- PDB-1pp4: The crystal structure of rhamnogalacturonan acetylesterase in spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pp4 | ||||||
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Title | The crystal structure of rhamnogalacturonan acetylesterase in space group P3121 | ||||||
Components | Rhamnogalacturonan acetylesterase | ||||||
Keywords | HYDROLASE / GDS(L) 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Molgaard, A. / Larsen, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase. Authors: Molgaard, A. / Larsen, S. #1: 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. #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.F. / Kauppinen, S. / Dalboge, H. / Johnsen, A.H. / Poulsen, J.C.N. / Larsen, S. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: A branched N-linked glycan at atomic resolution in the 1.12 A structure of rhamnogalacturonan acetylesterase Authors: Molgaard, A. / Larsen, S. #4: Journal: J.Biol.Chem. / Year: 1995 Title: Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus. Synergism between rhamnogalacturonan degrading enzymes Authors: Kauppinen, S. / Christgau, S. / Kofod, L.V. / Halkier, T. / Dorreich, K. / Dalboge, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pp4.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pp4.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1pp4 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1pp4 | HTTPS FTP |
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-Related structure data
Related structure data | 1deoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer represented by either the A or the B chain in the asymmetric unit |
-Components
#1: Protein | Mass: 24622.881 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus (mold) / Gene: RHA1 / Plasmid: PHD464 / Production host: Aspergillus oryzae (mold) / Strain (production host): KSM 510 References: UniProt: Q00017, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Sugar | ChemComp-NAG / #3: 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: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 4000, 2-propanol, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 15, 1996 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.6 Å / Num. all: 25036 / Num. obs: 24979 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 56.79 Å2 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.49→2.62 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.452 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1deo Resolution: 2.5→28.18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→28.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å /
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