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Yorodumi- PDB-2xfg: Reassembly and co-crystallization of a family 9 processive endogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xfg | ||||||
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Title | Reassembly and co-crystallization of a family 9 processive endoglucanase from separately expressed GH9 and CBM3c modules | ||||||
Components | (ENDOGLUCANASE 1) x 2 | ||||||
Keywords | HYDROLASE/SUGAR BINDING PROTEIN / HYDROLASE-SUGAR BINDING PROTEIN COMPLEX / FAMILY-9 GLYCOSIDE HYDROLASE / HYDROLASE / SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 Å | ||||||
Authors | Petkun, S. / Lamed, R. / Jindou, S. / Burstein, T. / Yaniv, O. / Shoham, Y. / Shimon, J.W.L. / Bayer, E.A. / Frolow, F. | ||||||
Citation | Journal: Peerj / Year: 2015 Title: Reassembly and Co-Crystallization of a Family 9 Processive Endoglucanase from its Component Parts: Structural and Functional Significance of Intermodular Linker Authors: Petkun, S. / Grinberg, I.R. / Lamed, R. / Jindou, S. / Burstein, T. / Yaniv, O. / Shoham, Y. / Shimon, J.W.L. / Bayer, E.A. / Frolow, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xfg.cif.gz | 409 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xfg.ent.gz | 339.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xfg_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 2xfg_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 2xfg_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 2xfg_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/2xfg ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xfg | HTTPS FTP |
-Related structure data
Related structure data | 1g87S S: Starting model for refinement |
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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: 52818.062 Da / Num. of mol.: 1 / Fragment: GH9 CATALYTIC DOMAIN, RESIDUES 54-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q02934, cellulase | ||||
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#2: Protein | Mass: 19581.607 Da / Num. of mol.: 1 / Fragment: CBM3C CELLULOSE BINDING MODULE, RESIDUES 517-683 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q02934 | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.37 Å3/Da / Density % sol: 48.17 % / Description: NONE |
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Crystal grow | pH: 8 Details: 24% PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→43.81 Å / Num. obs: 76727 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 34.72 |
Reflection shell | Resolution: 1.68→1.71 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.08 / % possible all: 74.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G87 Resolution: 1.679→20.868 Å / SU ML: 0.16 / σ(F): 0.02 / Phase error: 16.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.314 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.679→20.868 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.1181 Å / Origin y: -31.0663 Å / Origin z: 24.4566 Å
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Refinement TLS group | Selection details: ALL |