+Open data
-Basic information
Entry | Database: PDB / ID: 3x2k | |||||||||
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Title | X-ray structure of PcCel45A D114N with cellopentaose at 95K. | |||||||||
Components | Endoglucanase V-like protein | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information 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 Similarity search - Domain/homology | |||||||||
Biological species | Phanerochaete chrysosporium (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.182 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 | 3x2k.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x2k.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x2k_validation.pdf.gz | 864 KB | Display | wwPDB validaton report |
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Full document | 3x2k_full_validation.pdf.gz | 864.1 KB | Display | |
Data in XML | 3x2k_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 3x2k_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x2k ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x2k | HTTPS FTP |
-Related structure data
Related structure data | 3x2gC 3x2hC 3x2iC 3x2jC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18177.809 Da / Num. of mol.: 1 / Fragment: UNP residues 27-206 / Mutation: D114N 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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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose |
-Non-polymers , 3 types, 239 molecules
#4: Chemical | ChemComp-40S / #5: Chemical | #6: 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: 1.94 Å3/Da / Density % sol: 36.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 60% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, 5mM cellopentaose, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 47795 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.121 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 1.18→1.2 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.457 / % possible all: 71.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.182→26.448 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 11.21 / 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: 1.182→26.448 Å
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Refine LS restraints |
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LS refinement shell |
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