[English] 日本語

- PDB-1z3w: Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1z3w | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole | ||||||||||||
![]() | cellulase | ||||||||||||
![]() | HYDROLASE / Beta sandwich | ||||||||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ubhayasekera, W. / Vasella, A. / Stahlberg, J. / Mowbray, S.L. | ||||||||||||
![]() | ![]() Title: Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors Authors: Ubhayasekera, W. / Munoz, I.G. / Vasella, A. / Stahlberg, J. / Mowbray, S.L. #1: ![]() Title: Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes Authors: Munoz, I.G. / Ubhayasekera, W. / Henriksson, H. / Szabo, I. / Pettersson, G. / Johansson, G. / Mowbray, S.L. / Stahlberg, J. #2: ![]() Title: The catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: structural studies of its complex with the beta blocker (R)-propranolol Authors: Munoz, I.G. / Mowbray, S.L. / Stahlberg, J. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 178.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 819.8 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z3tC ![]() 1z3vC ![]() 1gpiS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45777.141 Da / Num. of mol.: 1 / Fragment: Catalytic module / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q7LIJ0, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
---|---|
#2: Sugar | ChemComp-NAG / |
#3: Sugar | ChemComp-IDC / ( |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: TRIS-HCl, calcium chloride, PEG 5000, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2001 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43 Å / Num. all: 39785 / Num. obs: 39785 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2685 / % possible all: 92.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GPI Resolution: 1.7→36.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.977 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.223 / ESU R Free: 0.119 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.761 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→36.27 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|