+Open data
-Basic information
Entry | Database: PDB / ID: 3x2n | ||||||
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Title | Proton relay pathway in inverting cellulase | ||||||
Components | Endoglucanase V-like protein | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta / Endoglucanase V-like protein Function and homology information | ||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 Å | ||||||
Authors | Nakamura, A. / Ishida, T. / Fushinobu, S. / Igarashi, K. / Samejima, M. | ||||||
Citation | Journal: Sci Adv / Year: 2015 Title: "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. Authors: Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Fushinobu, S. / Tanaka, I. / Kaneko, S. / Ohta, K. / Tanaka, H. / Inaka, K. / Higuchi, Y. / Niimura, N. / Samejima, M. / Igarashi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x2n.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x2n.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x2n_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3x2n_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 3x2n_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3x2n_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x2n ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x2n | HTTPS FTP |
-Related structure data
Related structure data | 3x2gC 3x2hC 3x2iC 3x2jC 3x2kC 3x2lC 3x2mC 3x2oC 3x2pC 4zm7C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18178.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: egv, PcCel45A / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B3Y002 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 3.0M Ammonium Sulphate, 20mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 44358 / Num. obs: 44001 / % possible obs: 99.2 % / Observed criterion σ(I): 663.6 / Redundancy: 3.6 % / Rsym value: 0.053 / Net I/σ(I): 34.92 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 15.96 / Num. unique all: 2204 / Rsym value: 0.085 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.2→27.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.785 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 7.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→27.92 Å
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Refine LS restraints |
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