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Yorodumi- PDB-6jhg: Crystal structure of apo Pullulanase from Paenibacillus barengolt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jhg | |||||||||
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Title | Crystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121 | |||||||||
Components | Pulullanase | |||||||||
Keywords | HYDROLASE / GH13 / Pullulanase | |||||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Paenibacillus barengoltzii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 Å | |||||||||
Authors | Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | |||||||||
Citation | Journal: To Be Published Title: Crystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121 Authors: Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jhg.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jhg.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jhg_validation.pdf.gz | 910 KB | Display | wwPDB validaton report |
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Full document | 6jhg_full_validation.pdf.gz | 914.8 KB | Display | |
Data in XML | 6jhg_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 6jhg_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/6jhg ftp://data.pdbj.org/pub/pdb/validation_reports/jh/6jhg | HTTPS FTP |
-Related structure data
Related structure data | 2e8yS 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: 75183.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-11 (MLSVQKEFHGT) and 638-657 (GASGEAAAAAPAAAGGPPAG) had low-level electron density and were not included in the model Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU940 / Plasmid: pET-28a(+) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0C5GWS2, pullulanase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.02M HEPES pH 6.5, 21% PEG 3350, 0.7% beta-OG / Temp details: 291-295 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.891→50 Å / Num. obs: 53244 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.551 |
Reflection shell | Resolution: 1.891→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 2669 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E8Y Resolution: 1.891→28.631 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.891→28.631 Å
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Refine LS restraints |
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LS refinement shell |
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