[English] 日本語
Yorodumi- PDB-4v2x: High resolution structure of the full length tri-modular endo-bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v2x | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution structure of the full length tri-modular endo-beta-1, 4-glucanase B (Cel5B) from Bacillus halodurans | ||||||
Components | ENDO-BETA-1,4-GLUCANASE (CELLULASE B) | ||||||
Keywords | HYDROLASE / TRI-MODULAR | ||||||
Function / homology | Function and homology information glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS HALODURANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Venditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Family 46 Carbohydrate-Binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and Beta-1,3-1,4-Glucans Through Distinct Mechanisms. Authors: Venditto, I. / Najmudin, S. / Luis, A.S. / Ferreira, L.M. / Sakka, K. / Knox, J.P. / Gilbert, H.J. / Fontes, C.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the Family 46 Carbohydrate-Binding Module (Cbm46) of Endo-Beta-1,4-Glucanase B (Celb) from Bacillus Halodurans. Authors: Venditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4v2x.cif.gz | 237.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4v2x.ent.gz | 188.5 KB | Display | PDB format |
PDBx/mmJSON format | 4v2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v2x_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4v2x_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 4v2x_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4v2x_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2x ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2x | HTTPS FTP |
-Related structure data
Related structure data | 4uz8C 4uznC 3ndzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68313.047 Da / Num. of mol.: 1 Fragment: FULL LENGTH CEL5B WITH CATALYTIC, IG-LIKE AND CBM46 MODULES, RESIDUES 1-574 Source method: isolated from a genetically manipulated source Details: DNA SOURCE BA000004 / Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KF82 |
---|
-Non-polymers , 5 types, 509 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CAC / | #6: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | CACODYLATE ION (CAC): FROM CRYSTALLISATION BUFFER CALCIUM ION (CA): FROM STORAGE BUFFER GLYCEROL ...CACODYLATE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE PH 6.5, 8% PEG 8K WITH 30% GLYCEROL ADDED TO ABOVE AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→51.27 Å / Num. obs: 66600 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NDZ Resolution: 1.64→51.27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.515 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. U VALUES WITH TLS ADDED. PDB_REDO WAS USED IN THE PENULTIMATE STAGE OF REFINEMENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.389 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→51.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|