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Yorodumi- PDB-1l8f: Structure of 20K-endoglucanase from Melanocarpus albomyces at 1.8 A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l8f | ||||||
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Title | Structure of 20K-endoglucanase from Melanocarpus albomyces at 1.8 A | ||||||
Components | Endoglucanase | ||||||
Keywords | HYDROLASE / cellulase / thermophilic / endoglucanase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Melanocarpus albomyces (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Valjakka, J. / Rouvinen, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of 20K endoglucanase from Melanocarpus albomyces at 1.8 A resolution. Authors: Valjakka, J. / Rouvinen, J. | ||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8f.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8f.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l8f_validation.pdf.gz | 418.1 KB | Display | wwPDB validaton report |
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Full document | 1l8f_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 1l8f_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1l8f_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8f ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8f | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22230.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Melanocarpus albomyces (fungus) / References: UniProt: Q8J0K8, cellulase |
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#2: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.98 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: peg 8000, Na-acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 24, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→99 Å / Num. all: 78044 / Num. obs: 76338 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 88.3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 99 Å / Num. obs: 16780 / Num. measured all: 78044 |
Reflection shell | *PLUS % possible obs: 88.3 % / Rmerge(I) obs: 0.251 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Data cutoff high rms absF: 10000 / σ(F): 0
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Solvent computation | Bsol: 67.3274 Å2 / ksol: 0.430727 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 500 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.1948 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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