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Yorodumi- PDB-1oa7: Structure of Melanocarpus albomyces endoglucanase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oa7 | |||||||||
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Title | Structure of Melanocarpus albomyces endoglucanase in complex with cellobiose | |||||||||
Components | CELLULASE | |||||||||
Keywords | HYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASES | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | MELANOCARPUS ALBOMYCES (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hirvonen, M. / Papageorgiou, A.C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of a Family 45 Endoglucanase from Melanocarpus Albomyces: Mechanistic Implications Based on the Free and Cellobiose-Bound Forms Authors: Hirvonen, M. / Papageorgiou, A.C. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oa7.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oa7.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oa7_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 1oa7_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 1oa7_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1oa7_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oa7 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oa7 | HTTPS FTP |
-Related structure data
Related structure data | 1oa9C 3engS C: citing same article (ref.) 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: 22932.221 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: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
#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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 4.6 / Details: PEG 4000 15% W/V, 0.15 M KOAC, 0.1 M NAOAC PH 4.6 |
Crystal grow | *PLUS Method: unknown / Details: Hirvonen, M., (2002) Acta Cryst., D58, 336. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2001 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 133688 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.6 / % possible all: 89.1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 13447 / Num. measured all: 133688 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 89.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ENG Resolution: 2→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1500347 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT / Bsol: 49.5 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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