+Open data
-Basic information
Entry | Database: PDB / ID: 1egz | ||||||
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Title | CELLULASE CEL5 FROM ERWINIA CHRYSANTHEMI, A FAMILY GH 5-2 ENZYME | ||||||
Components | ENDOGLUCANASE Z | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE / CLAN GH-A / FAMILY 5-2 / CELLULASE | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Erwinia chrysanthemi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Czjzek, M. / El Hassouni, M. / Py, B. / Barras, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Type II protein secretion in gram-negative pathogenic bacteria: the study of the structure/secretion relationships of the cellulase Cel5 (formerly EGZ) from Erwinia chrysanthemi Authors: Chapon, M. / Czjzek, M. / El Hassouni, M. / Py, B. / Juy, M. / Barras, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1egz.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1egz.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 1egz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1egz_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 1egz_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 1egz_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 1egz_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/1egz ftp://data.pdbj.org/pub/pdb/validation_reports/eg/1egz | HTTPS FTP |
-Related structure data
Related structure data | 1a3hS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32134.514 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Details: GENE: CELZ / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Cellular location: EXTERIOR / Secretion: TYPE II / References: UniProt: P07103, cellulase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | SECRETED (MATURE) PROTEIN, CONSISTING | |
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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: 2.08 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: VAPOR DIFFUSION HANGING DROP; PEG 4000 28%, TRIS PH 8.0 20 MM, MGSO4 20 MM, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995 |
Radiation | Monochromator: GRAPHITE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29 Å / Num. obs: 38365 / % possible obs: 98 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.134 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.45 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 98 % / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 97 % / Num. unique obs: 1749 / Rmerge(I) obs: 0.373 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A3H Resolution: 2.3→29 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0.5
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Displacement parameters | Biso mean: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 32807 / Rfactor obs: 0.187 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.261 |