+Open data
-Basic information
Entry | Database: PDB / ID: 4qaw | ||||||
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Title | Structure of modular Xyn30D from Paenibacillus barcinonensis | ||||||
Components | Xyn30D | ||||||
Keywords | HYDROLASE / Tim Barrel / Beta-Structure / Carbohydrate/Sugar Binding / Calcium Binding / Tim Barrel Beta-Structure / Carbohydrate/Sugar Binding Calcium Binding / plant-cell wall degradation | ||||||
Function / homology | Function and homology information glucosylceramidase activity / sphingolipid metabolic process / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paenibacillus barcinonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sainz-Polo, M.A. / Sanz-Aparicio, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity. Authors: Sainz-Polo, M.A. / Valenzuela, S.V. / Gonzalez, B. / Pastor, F.I. / Sanz-Aparicio, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qaw.cif.gz | 792.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qaw.ent.gz | 654.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qaw_validation.pdf.gz | 503.5 KB | Display | wwPDB validaton report |
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Full document | 4qaw_full_validation.pdf.gz | 532.9 KB | Display | |
Data in XML | 4qaw_validation.xml.gz | 130.5 KB | Display | |
Data in CIF | 4qaw_validation.cif.gz | 180.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qaw ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qaw | HTTPS FTP |
-Related structure data
Related structure data | 4qb1C 4qb2C 4qb6C 2vzpS 3gtnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 62184.691 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: xyn30d / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H6WCZ0, endo-1,4-beta-xylanase #2: Chemical | ChemComp-CA / #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: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 3350, 5% Glycerol, 0.1M Tris, Streak Seeding (2:1), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 4, 2011 | |||||||||||||||
Radiation | Monochromator: Horizontally diffracting monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→40.77 Å / Num. all: 243818 / Num. obs: 243713 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Rmerge(I) obs: 0.143 / Rsym value: 0.044 / Net I/σ(I): 14.7 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.178 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3GTN, 2VZP Resolution: 2.4→40.77 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.501 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.621 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40.77 Å
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Refine LS restraints |
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