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- PDB-1h5v: Thiopentasaccharide complex of the endoglucanase Cel5A from Bacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h5v | |||||||||
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Title | Thiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form | |||||||||
![]() | ENDOGLUCANASE 5A | |||||||||
![]() | HYDROLASE / CELLULASE / ENDOGLUCANASE / THIOOLIGOSACCHARIDE | |||||||||
Function / homology | ![]() cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Varrot, A. / Sulzenbacher, G. / Schulein, M. / Driguez, H. / Davies, G.J. | |||||||||
![]() | ![]() Title: Atomic Resolution Structure of Endoglucanase Cel5A in Complex with Methyl 4,4II,4III,4Iv-Tetrathio-Alpha-Cellopentoside Highlights the Alternative Binding Modes Targeted by Substrate Mimics Authors: Varrot, A. / Schulein, M. / Fruchard, S. / Driguez, H. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.4 KB | Display | ![]() |
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PDB format | ![]() | 127.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qhzS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34118.168 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN RESIDUES 27-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)- ...alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside Type: oligosaccharide / Mass: 923.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.6 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Mar 15, 2000 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: DIAMOND(111)GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. obs: 155682 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7 |
Reflection | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Redundancy: 3.6 % |
Reflection shell | *PLUS % possible obs: 98.7 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QHZ Resolution: 1.1→20 Å / SU B: 0.72227 / SU ML: 0.01778 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.03223 / Details: THE FIRST THREE RESIDUES DUE TO DISORD
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.12 / Rfactor Rfree: 0.138 / Rfactor Rwork: 0.12 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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