+Open data
-Basic information
Entry | Database: PDB / ID: 3x2i | ||||||
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Title | X-ray structure of PcCel45A N92D apo form at 298K. | ||||||
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 / 3-methylpentane-1,5-diol / Endoglucanase V-like protein Function and homology information | ||||||
Biological species | Phanerochaete chrysosporium (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Nakamura, A. / Ishida, T. / Samejima, M. / Igarashi, K. | ||||||
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 | 3x2i.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x2i.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x2i_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 3x2i_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 3x2i_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3x2i_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x2i ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x2i | HTTPS FTP |
-Related structure data
Related structure data | 3x2gC 3x2hC 3x2jC 3x2kC 3x2lC 3x2mC 3x2nC 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
#1: Protein | Mass: 18179.777 Da / Num. of mol.: 1 / Fragment: UNP residues 27-206 / Mutation: N92D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: egv, PcCel45A / Plasmid: pPICZa / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B3Y002 |
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#2: Chemical | ChemComp-40S / |
#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: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 65% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 23719 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rsym value: 0.118 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 3625 / Rsym value: 0.253 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.501 Å / SU ML: 0.1 / σ(F): 1.56 / Phase error: 12.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→43.501 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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