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- PDB-1w1y: Crystal structure of S. marcescens chitinase B in complex with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w1y | ||||||
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Title | Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(L-Tyr-L-Pro) at 1.85 A resolution | ||||||
![]() | CHITINASE B | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / CHITINASE / STRUCTURE-BASED INHIBITOR DESIGN / CYCLIC DIPEPTIDE | ||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Houston, D.R. / Synstad, B. / Eijsink, V.G.H. / Eggleston, I. / Van Aalten, D.M.F. | ||||||
![]() | ![]() Title: Structure-Based Exploration of Cyclic Dipeptide Chitinase Inhibitors Authors: Houston, D.R. / Synstad, B. / Eijsink, V.G.H. / Stark, M.J. / Eggleston, I. / Van Aalten, D.M.F. | ||||||
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. DETERMINATION METHOD: DSSP 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 | ![]() | 232.7 KB | Display | ![]() |
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PDB format | ![]() | 187.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 49.3 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w1pC ![]() 1w1tC ![]() 1w1vC ![]() 1o6iS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 55518.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-TYP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 7 Details: 1.5 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7, 25 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. obs: 89533 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.69 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 32.22 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.32 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O6I Resolution: 1.85→24.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2739093.61 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 43.0464 Å2 / ksol: 0.368874 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.61 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→24.91 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.85 Å |