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- PDB-6mi1: CRYSTAL STRUCTURE ANALYSIS OF THE VARIANT PLANT EXOHYDROLASE ARG1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mi1 | ||||||||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE VARIANT PLANT EXOHYDROLASE ARG158ALA-GLU161ALA IN COMPLEX WITH METHYL 6-THIO-BETA-GENTIOBIOSIDE | ||||||||||||
![]() | Beta-D-glucan exohydrolase isoenzyme ExoI | ||||||||||||
![]() | HYDROLASE / BETA BARREL / GRAIN DEVELOPMENT / TIM BARREL/BETA SHEET / N-GLYCOSYLATION / PLANT APOPLAST | ||||||||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Streltsov, V.A. / Luang, S. / Hrmova, M. | ||||||||||||
![]() | ![]() Title: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / ...Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / Mendoza, F. / Tiessler-Sala, L. / Sanchez-Aparicio, J.E. / Rodriguez-Guerra, J. / Lluch, J.M. / Marechal, J.D. / Masgrau, L. / Hrmova, M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.4 KB | Display | ![]() |
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PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.3 KB | Display | ![]() |
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Full document | ![]() | 854.7 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wlhC ![]() 3wliC ![]() 3wljC ![]() 3wlkC ![]() 3wllC ![]() 3wlmC ![]() 3wlnC ![]() 3wloC ![]() 3wlpC ![]() 3wlqC ![]() 3wlrC ![]() 6md6C ![]() 1ieqS ![]() 3wlt S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65749.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-627 / Mutation: ARG158ALA, GLU161ALA Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PPICZALPHABNH8/DEST / Production host: ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside / METHYL 6-THIO-BETA-GENTIOBIOSIDE |
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#3: Sugar |
-Non-polymers , 3 types, 343 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING OF AF102868 (GENBANK ACCESSION NUMBER). ...THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.13 % |
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Crystal grow | Temperature: 278 K / Method: evaporation / pH: 7 Details: 75MM HEPES-NAOH PH7.0, 1.2% PEG 400, 1.7M AMMONIUM SULPHATE , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2013 / Details: COLLIMATING MIRROR |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→88.96 Å / Num. obs: 41138 / % possible obs: 99.3 % / Redundancy: 28 % / Net I/σ(I): 68.4 |
Reflection shell | Resolution: 2.3→2.36 Å / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IEQ Resolution: 2.3→39.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.372 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.832 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.13 Å
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Refine LS restraints |
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