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Yorodumi- PDB-1oa2: Comparison of Family 12 Glycoside Hydrolases and Recruited Substi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oa2 | |||||||||
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Title | Comparison of Family 12 Glycoside Hydrolases and Recruited Substitutions Important for Thermal Stability | |||||||||
Components | ENDO-BETA-1,4-GLUCANASE | |||||||||
Keywords | HYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12 / TRICHODERMA REESEI CEL12A | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | TRICHODERMA REESEI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Sandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Day, A.G. / Jones, T.A. / Mitchinson, C. | |||||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Comparison of Family 12 Glycoside Hydrolases and Recruited Substitutions Important for Thermal Stability Authors: Sandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Day, A.G. / Jones, T.A. / Mitchinson, C. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oa2.cif.gz | 261.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oa2.ent.gz | 214.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oa2 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oa2 | HTTPS FTP |
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-Related structure data
Related structure data | 1oa3C 1oa4C 1h8vS S: Starting model for refinement 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 23501.395 Da / Num. of mol.: 6 / Fragment: RESIDUES 17-234 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: O00095, cellulase #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Compound details | ENDOHYDROL | Sequence details | GLN 17 MODIFIED RESIDUE | |
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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 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-24 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. obs: 172895 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rsym value: 0.037 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.38 / % possible all: 93 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 25 Å / % possible obs: 94.4 % / Num. measured all: 490560 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 94.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8V Resolution: 1.5→20 Å / SU B: 2.56872 / SU ML: 0.09565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15274 / ESU R Free: 0.12287 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 17.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refinement | *PLUS Rfactor Rfree: 0.219 / Rfactor Rwork: 0.201 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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