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Yorodumi- PDB-4uqd: X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uqd | ||||||
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Title | X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.25 A resolution | ||||||
Components | CARBOHYDRATE BINDING FAMILY 6 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information glucosylceramidase activity / sphingolipid metabolic process / polysaccharide catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | RUMINICLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Freire, F. / Verma, A.K. / Goyal, A. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uqd.cif.gz | 197.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uqd.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqd ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqd | HTTPS FTP |
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-Related structure data
Related structure data | 4ckqSC 4uq9C 4uqaC 4uqbC 4uqcC 4uqeC 5a6lC 5a6mC 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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1 |
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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.) RUMINICLOSTRIDIUM THERMOCELLUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: E6UTM3, UniProt: A3DJS9*PLUS, endo-1,4-beta-xylanase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-THR / | #5: 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: 2.13 Å3/Da / Density % sol: 42.4 % / Description: NONE |
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Crystal grow | Details: 25 % (V/V) PEG 3350, 0.2 M CACL2, 0.1 M HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537 |
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: 1.25→50.9 Å / Num. obs: 96003 / % possible obs: 89.8 % / Observed criterion σ(I): 1.58 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.21 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.58 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CKQ Resolution: 1.25→42.63 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.51 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / 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: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.003 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→42.63 Å
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Refine LS restraints |
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