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- PDB-1ur9: Interactions of a family 18 chitinase with the designed inhibitor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ur9 | |||||||||
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Title | Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone | |||||||||
![]() | CHITINASE B | |||||||||
![]() | HYDROLASE / CHITINASE / INHIBITION / LACTONE / CHITIN DEGRADATION / GLYCOSIDASE | |||||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vaaje-Kolstad, G. / Vasella, A. / Peter, M.G. / Netter, C. / Houston, D.R. / Westereng, B. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F. | |||||||||
![]() | ![]() Title: Interactions of a Family 18 Chitinase with the Designed Inhibitor Hm508 and its Degradation Product, Chitobiono-Delta-Lactone. Authors: Vaaje-Kolstad, G. / Vasella, A. / Peter, M.G. / Netter, C. / Houston, D.R. / Westereng, B. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F. #1: ![]() Title: Structural Insights Into the Catalytic Mechansim of a Family 18 Exochitinase Authors: Van Aalten, D.M.F. / Komander, D. / Synstad, B. / Gaseidnes, S. / Peter, M.G. / Eijsink, V.G.H. #2: ![]() Title: Structure of a Two-Domain Chitotriosidase from Serratia Marcescens at 1.9 A Resolution Authors: Van Aalten, D.M.F. / Synstad, B. / Brurberg, M.B. / Hough, E. / Riise, B. / Eijsink, V.G.H. / Wierenga, R.K. | |||||||||
History |
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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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.1 KB | Display | ![]() |
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PDB format | ![]() | 192.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 53.5 KB | Display | |
Data in CIF | ![]() | 77.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ur8C ![]() 1goiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 55603.145 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 929 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PHJ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PHJ.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | pH: 7 Details: 100 MM HEPES PH 7.0, 15% GLYCEROL, 1.3 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 97967 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / % possible all: 77.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GOI Resolution: 1.8→24.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2048263.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SOME SIDECHAIN ATOMS HAVE BEEN OMITTED DUE TO MISSING OR AMBIGUOUS ELECTRON DENSITY. THESE ATOMS ARE LISTED IN REMARK 470
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.0995 Å2 / ksol: 0.338994 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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