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Yorodumi- PDB-1ajk: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ajk | ||||||
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Title | CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84 | ||||||
Components | CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE | ||||||
Keywords | HYDROLASE / GLUCANASE / CIRCULAR PERMUTATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paenibacillus macerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ay, J. / Heinemann, U. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Crystal structures and properties of de novo circularly permuted 1,3-1,4-beta-glucanases. Authors: Ay, J. / Hahn, M. / Decanniere, K. / Piotukh, K. / Borriss, R. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ajk.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ajk.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ajk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1ajk ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1ajk | HTTPS FTP |
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-Related structure data
Related structure data | 1ajoC 2ayhS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.82105, -0.03541, -0.56976), Vector: |
-Components
#1: Protein | Mass: 23935.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus macerans (bacteria) / Cell line: DH5ALPHA / Plasmid: PTZ19R / Cell line (production host): DH5ALPHA / Production host: Escherichia coli (E. coli) / References: UniProt: P23904, licheninase #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | BOTH INDEPENDENT MOLECULES OF CPA16M-84 SHOW A CATION BINDING SITE WITH A CALCIUM ION IN OCTAHEDRAL ...BOTH INDEPENDEN | |
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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: 2.1 Å3/Da / Density % sol: 41 % Description: ONE LOW- AND ONE HIGH-RESOLUTION DATA SET WERE COLLECTED FROM ONE CRYSTAL. | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, ...Details: SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→33.33 Å / Num. obs: 38698 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.16 / % possible all: 94.4 |
Reflection | *PLUS Num. measured all: 132154 |
Reflection shell | *PLUS % possible obs: 94.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AYH Resolution: 1.8→33.33 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 33.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.33 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 35910 / Rfactor all: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |