[English] 日本語
Yorodumi- PDB-1w1p: Crystal structure of S. marcescens chitinase B in complex with th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w1p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(Gly-L-Pro) at 2.1 A resolution | ||||||
Components | CHITINASE B | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / CHITINASE / STRUCTURE-BASED INHIBITOR DESIGN / CYCLIC DIPEPTIDE | ||||||
Function / homology | Function and homology information chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Houston, D.R. / Synstad, B. / Eijsink, V.G.H. / Eggleston, I. / Van Aalten, D.M.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 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 |
| ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1w1p.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1w1p.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 1w1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w1p_validation.pdf.gz | 483.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1w1p_full_validation.pdf.gz | 499.4 KB | Display | |
Data in XML | 1w1p_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 1w1p_validation.cif.gz | 72.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w1p ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1p | HTTPS FTP |
-Related structure data
Related structure data | 1w1tC 1w1vC 1w1yC 1o6iS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55518.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q54276, chitinase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
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: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 57855 / % possible obs: 89.7 % / Observed criterion σ(I): 1 / Redundancy: 3.22 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.79 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.3 / % possible all: 90.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WWPDB ENTRY 1O6I Resolution: 2.1→24.91 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2543996.39 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 53.9279 Å2 / ksol: 0.334367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|