[English] 日本語
![](img/lk-miru.gif)
- PDB-4d5v: Hypocrea jecorina cellobiohydrolase Cel7A E217Q soaked with xylot... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4d5v | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Hypocrea jecorina cellobiohydrolase Cel7A E217Q soaked with xylotetraose. | ||||||||||||
![]() | CELLULOSE 1,4-BETA-CELLOBIOSIDASE | ||||||||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / CELLOBIOHYDROLASE / CELLULASE. INHIBITION / XYLOOLIGOSACCHARIDES | ||||||||||||
Function / homology | ![]() cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Momeni, M.H. / Stahlberg, J. / Hansson, H. | ||||||||||||
![]() | ![]() Title: Structural Insights Into the Inhibition of Cellobiohydrolase Cel7A by Xylooligosaccharides. Authors: Haddad Momeni, M. / Ubhayasekera, W. / Sandgren, M. / Stahlberg, J. / Hansson, H. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 114 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 983.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 985.8 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d5iC ![]() 4d5jC ![]() 4d5oC ![]() 4d5pC ![]() 4d5qC ![]() 7celS C: citing same article ( S: Starting model for refinement |
---|---|
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: 46067.754 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 18-451 / Mutation: YES [E217Q] Source method: isolated from a genetically manipulated source Details: THE STRUCTURE CONTAINS ONE XYLOTETRAOSE MOLECULE BOUND AT SUBSITES -7 TO -3, AND AN OPEN XYLOBIOSYL MOLECULE BOUND AT SUBSITES -2 TO -1 AT PARTIAL OCCUPANCY. Source: (gene. exp.) ![]() Description: HYPOCREA JECORINA WAS PREVIOUSLY KNOWN AS TRICHODERMA REESEI. Variant: VTT-D-93201 / Plasmid: PEM-F5 / Production host: ![]() References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (reducing end) |
---|
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | beta-D-xylopyranose-(1-4)-D-xylose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 530 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CO / |
---|---|
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | COBALT (II) ION (CO): 10 MM COBALT CHLORIDE WAS PRESENT IN CRYSTALLISATION SOLUTION PYROGLUTAMIC ...COBALT (II) ION (CO): 10 MM COBALT CHLORIDE WAS PRESENT IN CRYSTALLIS |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12.5% GLYCEROL, VAPOR DIFFUSION - HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Sep 24, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.041 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→29.45 Å / Num. obs: 48981 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.62→1.71 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 96.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 7CEL Resolution: 1.62→66.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.519 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / 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 REFINED INDIVIDUALLY THE STRUCTURE CONTAINS ONE XYLOTETRAOSE MOLECULE BOUND AT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY THE STRUCTURE CONTAINS ONE XYLOTETRAOSE MOLECULE BOUND AT SUBSITES -7 TO -3, AND AN OPEN XYLOBIOSYL MOLECULE BOUND AT SUBSITES -2 TO -1 AT PARTIAL OCCUPANCY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 11.766 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→66.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|