[English] 日本語
Yorodumi- PDB-1kwf: Atomic Resolution Structure of an Inverting Glycosidase in Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kwf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Atomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate | |||||||||
Components | Endoglucanase A | |||||||||
Keywords | HYDROLASE / inverting glycosidase / atomic resolution / protein-carbohydrate interactions / reaction mechanism / cellulase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.94 Å | |||||||||
Authors | Guerin, D.M.A. / Lascombe, M.-B. / Costabel, M. / Souchon, H. / Lamzin, V. / Beguin, P. / Alzari, P.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. Authors: Guerin, D.M. / Lascombe, M.B. / Costabel, M. / Souchon, H. / Lamzin, V. / Beguin, P. / Alzari, P.M. #1: Journal: Structure / Year: 1996 Title: The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Authors: Alzari, P.M. / Souchon, H. / Dominguez, R. #2: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1996 Title: Crystallization of a family 8 cellulase from Clostridium thermocellum Authors: Souchon, H. / Beguin, P. / Alzari, P.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kwf.cif.gz | 181.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kwf.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kwf ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kwf | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40329.324 Da / Num. of mol.: 1 / Fragment: catalytic core (residues 33-395) / Mutation: E95Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: celA / Plasmid: pCT128 / Production host: Escherichia coli (E. coli) / Strain (production host): NCIB 10682 References: UniProt: P04955, UniProt: A3DC29*PLUS, cellulase | ||||
---|---|---|---|---|---|
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose | ||||
#3: Sugar | #4: Water | ChemComp-HOH / | Nonpolymer details | THE OBSERVED DENSITY FOR THE HET GROUP BGC IS INTERPRETED AS TWO CHAINS, ONE CORRESPONDING TO THE ...THE OBSERVED DENSITY FOR THE HET GROUP BGC IS INTERPRETE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.07 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 Details: used microseeding, Souchon, H., (1996) PROTEINS: STRUCT.,FUNCT.,GENET., 25, 134. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8815 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8815 Å / Relative weight: 1 |
Reflection | Resolution: 0.94→30 Å / Num. all: 208140 / Num. obs: 208140 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 0.94→0.95 Å / Rmerge(I) obs: 0.19 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 903691 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 0.94→10 Å / Num. parameters: 32403 / Num. restraintsaints: 41731 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 132 / Occupancy sum hydrogen: 2644 / Occupancy sum non hydrogen: 3345.45 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.94→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rwork: 0.094 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 0.94 Å / Lowest resolution: 0.97 Å / Rfactor Rwork: 0.135 / Num. reflection obs: 19946 / Rfactor obs: 0.135 |