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Yorodumi- PDB-7xks: Crystal structure of an alkaline pectate lyase from Bacillus clausii -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xks | ||||||
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Title | Crystal structure of an alkaline pectate lyase from Bacillus clausii | ||||||
Components | Pectate lyase | ||||||
Keywords | LYASE / alkaline pectate | ||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Alkalihalobacillus clausii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Zhou, C. / Zheng, Y.Y. / Liu, W.D. / Ma, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming. Authors: Zhou, C. / Cao, Y. / Xue, Y. / Liu, W. / Ju, J. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xks.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xks.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xks_validation.pdf.gz | 893.4 KB | Display | wwPDB validaton report |
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Full document | 7xks_full_validation.pdf.gz | 894.1 KB | Display | |
Data in XML | 7xks_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7xks_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/7xks ftp://data.pdbj.org/pub/pdb/validation_reports/xk/7xks | HTTPS FTP |
-Related structure data
Related structure data | 3vmwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33623.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalihalobacillus clausii (bacteria) / Gene: pelA / Plasmid: PET28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0P0J4R7, pectate lyase | ||||||
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#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05M Mgcl2, 0.1M HEPEs, 30% PEG 550 |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→30 Å / Num. obs: 26611 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 21.04 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Χ2: 1.768 / Net I/σ(I): 11.8 / Num. measured all: 276885 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VMW Resolution: 1.78→27.27 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.15 Å2 / Biso mean: 22.5313 Å2 / Biso min: 11.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.78→27.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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