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Yorodumi- PDB-1f5j: CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f5j | ||||||
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Title | CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION | ||||||
Components | BETA-1,4-XYLANASE | ||||||
Keywords | HYDROLASE / Xylanase / beta-barrel | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | Dictyoglomus thermophilum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | McCarthy, A.A. / Baker, E.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution. Authors: McCarthy, A.A. / Morris, D.D. / Bergquist, P.L. / Baker, E.N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallography & NMR system: A new software suite for macromolecular structure determination Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f5j.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f5j.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f5j_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 1f5j_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 1f5j_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1f5j_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f5j ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f5j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22310.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyoglomus thermophilum (bacteria) / Strain: RT46B.1 / Plasmid: PJLA602 / Production host: Escherichia coli (E. coli) / References: UniProt: P77853, endo-1,4-beta-xylanase #2: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.36 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.5-1.6 M ammonium sulphate, 0.2 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 207114 / Num. obs: 34109 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 0.307 / % possible all: 97 |
Reflection | *PLUS Num. measured all: 207114 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Resolution: 1.8→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1922542.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.18 Å2 / ksol: 0.417 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.245 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.206 |