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Yorodumi- PDB-3wp5: The crystal structure of mutant CDBFV E109A from Neocallimastix p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wp5 | ||||||
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Title | The crystal structure of mutant CDBFV E109A from Neocallimastix patriciarum | ||||||
Components | CDBFV | ||||||
Keywords | HYDROLASE / xylanase / regulatory N-terminal region / disulfide bond / industrial enzyme / beta-jellyroll fold | ||||||
Function / homology | Function and homology information cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Neocallimastix patriciarum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Cheng, Y.S. / Chen, C.C. / Huang, C.H. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural analysis of a glycoside hydrolase family 11 xylanase from Neocallimastix patriciarum: insights into the molecular basis of a thermophilic enzyme. Authors: Cheng, Y.S. / Chen, C.C. / Huang, C.H. / Ko, T.P. / Luo, W. / Huang, J.W. / Liu, J.R. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wp5.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wp5.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wp5 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wp5 | HTTPS FTP |
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-Related structure data
Related structure data | 3wp4SC 3wp6C S: Starting model for refinement C: citing same article (ref.) |
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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: 24634.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neocallimastix patriciarum (fungus) / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9UV68*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS PROTEIN HAS MUTATION E109A |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium cacodylate, pH 6.5, 0.2M ammonium sulfate, 26% PEG 8000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→25 Å / Num. obs: 50174 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5000 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WP4 Resolution: 1.32→24.86 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.434 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 14.931 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→24.86 Å
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Refine LS restraints |
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