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Yorodumi- PDB-1w1t: Crystal structure of S. marcescens chitinase B in complex with th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w1t | ||||||
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Title | Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(His-L-Pro) at 1.9 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: 1.9 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w1t.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w1t.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w1t ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1t | HTTPS FTP |
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-Related structure data
Related structure data | 1w1pC 1w1vC 1w1yC 1o6iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q54276, chitinase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CHQ / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49 % |
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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: 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: 1.9→25 Å / Num. obs: 85317 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.91 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.31 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O6I Resolution: 1.9→24.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2669843.24 / 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: 48.6515 Å2 / ksol: 0.356394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.88 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.9 Å |