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Yorodumi- PDB-8a3h: Cellobiose-derived imidazole complex of the endoglucanase cel5A f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a3h | |||||||||
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Title | Cellobiose-derived imidazole complex of the endoglucanase cel5A from Bacillus agaradhaerens at 0.97 A resolution | |||||||||
Components | PROTEIN (ENDOGLUCANASE) | |||||||||
Keywords | HYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 5 / ENDOGLUCANASE / TRANSITION STATE ANALOGUE / LATERAL PROTONATION | |||||||||
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 / SYNCHROTRON / OTHER / Resolution: 0.97 Å | |||||||||
Authors | Varrot, A. / Schulein, M. / Pipelier, M. / Vasella, A. / Davies, G.J. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1999 Title: Lateral Protonation of a Glycosidase Inhibitor. Structure of the Bacillus agaradhaerens Cel5A in Complex with a Cellobiose-Derived Imidazole at 0.97 A Resolution Authors: Varrot, A. / Schulein, M. / Pipelier, M. / Vasella, A. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a3h.cif.gz | 146.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a3h.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a3h_validation.pdf.gz | 483.7 KB | Display | wwPDB validaton report |
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Full document | 8a3h_full_validation.pdf.gz | 493.1 KB | Display | |
Data in XML | 8a3h_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 8a3h_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a3h ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a3h | 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 33998.023 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 (NCIMB 40482) / Plasmid: THERRAMYL-AMYLASE PROMOTER SYSTEM / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306 References: UniProt: P06565, UniProt: O85465*PLUS, cellulase |
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#4: Sugar | ChemComp-IDC / ( |
-Non-polymers , 4 types, 508 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-ACT / | ||
#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Details
Compound details | THE THREE FIRST RESIDUES ARE DISORDERED SO SEQUENCE STARTS AT RESIDUE SER A 4 . THIS IS THE ...THE THREE FIRST RESIDUES ARE DISORDERED |
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Nonpolymer details | THE IMIDAZOLE-DERIVED CELLOBIOSIDE IS BOUND IN THE -2 AND -1 SUBSITE. THE IMIDAZOLE RING SITE IN ...THE IMIDAZOLE-DERIVED CELLOBIOSI |
Sequence details | THE FIRST 26 RESIDUES IN THE DATABASE CORRESPONDS TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | pH: 5.5 Details: PROTEIN CONCENTRATION 20 MG/ML, 2 M AMMONIUM SULPHATE, 100 MM SODIUM CITRATE PH 5.5, 10% GLYCEROL |
Crystal grow | *PLUS Method: other / Details: Murshudov, G.N., (1997) Acta Cryst., D53, 240. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 |
Detector | Date: Oct 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→30 Å / Num. obs: 149215 / % possible obs: 93 % / Redundancy: 5.3 % / Biso Wilson estimate: 6.44 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.321 / % possible all: 54 |
Reflection | *PLUS % possible obs: 93 % / Redundancy: 5.4 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 0.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1 / Rfactor Rfree: 0.12 / Rfactor Rwork: 0.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.034 |