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Yorodumi- PDB-1a3h: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3h | ||||||
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Title | ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION | ||||||
Components | ENDOGLUCANASECellulase | ||||||
Keywords | HYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5 | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus agaradhaerens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.57 Å | ||||||
Authors | Davies, G.J. / Brzozowski, A.M. / Andersen, K. / Schulein, M. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution Authors: Davies, G.J. / Dauter, M. / Brzozowski, A.M. / Bjornvad, M.E. / Andersen, K.V. / Schulein, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3h.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3h.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3h ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3h | HTTPS FTP |
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-Related 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: 33653.746 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 / Plasmid: THERMAMYL-AMYLASE PROMOTER SYSTEM / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase |
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#2: Water | ChemComp-HOH / |
Compound details | THE FIRST 3 RESIDUES ARE DISORDERED SO IT STARTS WITH RESIDUE SER 4. THIS THE NATURALLY OCCURRING ...THE FIRST 3 RESIDUES ARE DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 44 % | |||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: LONG MIRRORS (MSC) |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→15 Å / Num. obs: 222447 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.57→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 8 / Rsym value: 0.196 / % possible all: 98.4 |
Reflection shell | *PLUS % possible obs: 98.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.57→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.013 LOW RESOLUTION CUTOFF (A) : 15 FIT/AGREEMENT OF MODEL WITH ALL DATA. R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL R VALUE (WORKING ...Details: ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.013 LOW RESOLUTION CUTOFF (A) : 15 FIT/AGREEMENT OF MODEL WITH ALL DATA. R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL R VALUE (WORKING SET, NO CUTOFF) : 0.12888 FREE R VALUE (NO CUTOFF) : 0.16078
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Displacement parameters | Biso mean: 13.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 15 Å / Luzzati sigma a obs: 0.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |