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- PDB-4uqb: X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uqb | ||||||
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Title | X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.68 A resolution | ||||||
![]() | CARBOHYDRATE BINDING FAMILY 6 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() glucosylceramidase activity / sphingolipid metabolic process / polysaccharide catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Freire, F. / Verma, A.K. / Goyal, A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
![]() | ![]() Title: Conservation in the Mechanism of Glucuronoxylan Hydrolysis Revealed by the Structure of Glucuronoxylan Xylano-Hydrolase (Ctxyn30A) from Clostridium Thermocellum Authors: Freire, F. / Verma, A.K. / Bule, P. / Alves, V.D. / Fontes, C.M.G.A. / Goyal, A. / Najmudin, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.5 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ckqSC ![]() 4uq9C ![]() 4uqaC ![]() 4uqcC ![]() 4uqdC ![]() 4uqeC ![]() 5a6lC ![]() 5a6mC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46454.062 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CATALYTIC MODULE, RESIDUES 34-419 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: E6UTM3, UniProt: A3DJS9*PLUS, endo-1,4-beta-xylanase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES 7.5, 10 % (V/V)PEG 8000, 8 % (V/V)ETHILE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2014 Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50.68 Å / Num. obs: 47651 / % possible obs: 92.3 % / Observed criterion σ(I): 1.77 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.63 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.77 / % possible all: 77.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CKQ Resolution: 1.68→45.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.952 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→45.49 Å
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Refine LS restraints |
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