+Open data
-Basic information
Entry | Database: PDB / ID: 6aii | ||||||
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Title | Catalytic domain of PdAgaC | ||||||
Components | Beta-agarase | ||||||
Keywords | LYASE / Agarase | ||||||
Function / homology | Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Persicobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Teh, A.H. / Fazli, N.H. | ||||||
Funding support | Malaysia, 1items
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Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2020 Title: Crystal structure of a neoagarobiose-producing GH16 family beta-agarase from Persicobacter sp. CCB-QB2. Authors: Teh, A.H. / Fazli, N.H. / Furusawa, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aii.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aii.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aii ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aii | HTTPS FTP |
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-Related structure data
Related structure data | 4asmS 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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Unit cell |
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-Components
#1: Protein | Mass: 38439.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WP_053404800.1 / Source: (gene. exp.) Persicobacter (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-CA / |
#3: 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: 3.18 Å3/Da / Density % sol: 61.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14% PEG 20,000, 0.1 M sodium HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→34.34 Å / Num. obs: 62074 / % possible obs: 98.9 % / Redundancy: 7.39 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.4 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ASM Resolution: 1.63→34.34 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.377 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.056 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→34.34 Å
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Refine LS restraints |
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