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- PDB-4afm: Structural and biochemical characterization of a novel Carbohydra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4afm | ||||||
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Title | Structural and biochemical characterization of a novel Carbohydrate Binding Module of endoglucanase Cel5A from Eubacterium cellulosolvens. | ||||||
![]() | ENDOGLUCANASE CEL5A | ||||||
![]() | HYDROLASE / CARBOHYDRATE BINDING MODULE / FAMILY 5 GLYCOSIDE HYDROLASE | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luis, A.S. / Venditto, I. / Prates, J.A.M. / Ferreira, L.M.A. / Gilbert, H.J. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
![]() | ![]() Title: Understanding How Non-Catalytic Carbohydrate Binding Modules Can Display Specificity for Xyloglucan. Authors: Luis, A.S. / Venditto, I. / Prates, J.A.M. / Ferrieira, L.M.A. / Temple, M.J. / Rogowski, A. / Basle, A. / Xue, J. / Knox, J.P. / Najmudin, S. / Fontes, C.M.G.A. / Gilbert, H.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of a Novel Carbohydrate-Binding Module of Endoglucanase Cel5A from Eubacterium Cellulosolvens. Authors: Luis, A.S. / Alves, V.D. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ypjC ![]() 4aekSC ![]() 4aemC ![]() 4afdC ![]() 4ba6C C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14879.080 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 37-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Nonpolymer details | GLYCEROL (GOL): FROM THE CRYOPROTEC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | Temperature: 292 K / pH: 4.6 Details: 80 MG/ML OF PROTEIN AT 292 K WERE GROWN IN 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 26% W/V PEG 2K MME. CRYSTALS WERE SOAKED WITH 10 MM CELLOHEXAOSE FOR A FEW HOURS. ...Details: 80 MG/ML OF PROTEIN AT 292 K WERE GROWN IN 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 26% W/V PEG 2K MME. CRYSTALS WERE SOAKED WITH 10 MM CELLOHEXAOSE FOR A FEW HOURS. 30% GLYCEROL WAS USED AS A CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→38.74 Å / Num. obs: 35557 / % possible obs: 91.2 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4 / % possible all: 62.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AEK Resolution: 1.25→38.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.074 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES.PHENIX-1.7.2-869 WAS USED IN THE PENULTIMATE STEP FOR OCCUPANCY REFINEMENT AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES.PHENIX-1.7.2-869 WAS USED IN THE PENULTIMATE STEP FOR OCCUPANCY REFINEMENT AND TLS GROUP DETERMINATION. RESIDUES 37-38 AND 166-170 ARE DISORDERED. ASP A118 WAS MODELLED WITH ALTERNATE CONFORMATION. IT MAY ALSO HAVE RADIATION DAMAGE AS IN PDB 4AFD. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY. FOLLOWING WERE GIVEN ALTERNATE CONFORMATIONS, SER A45, GLU A51, GLN A67, GLN A71, MSE A73, GLU A82, ILE A83, IL3 A95 GLU A100, SER A103, SER A112, VAL A116, GLN A126, LYS A130, MSE A154, VAL A160 AND SER A162.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.031 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→38.7 Å
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Refine LS restraints |
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