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Yorodumi- PDB-1w9p: Specificity and affinity of natural product cyclopentapeptide inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w9p | ||||||
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Title | Specificity and affinity of natural product cyclopentapeptide inhibitors against Aspergillus fumigatus, human and bacterial chitinaseFra | ||||||
Components | CHITINASE | ||||||
Keywords | HYDROLASE / CHITINASE / PEPTIDE INHIBITORS / ARGIFIN / ARGADIN / GLYCOSIDASE | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Hodkinson, M. / Adams, D.J. / Shiomi, K. / Omura, S. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Chem.Biol. / Year: 2005 Title: Specificity and Affinity of Natural Product Cyclopentapeptide Inhibitors Against Aspergillus Fumigatus, Human and Bacterial Chitinases Authors: Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Hodkinson, M. / Adams, D.J. / Shiomi, K. / Omura, S. / 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 | 1w9p.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9p.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9p ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9p | HTTPS FTP |
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-Related structure data
Related structure data | 1w9uC 1w9vC 1wawC 1wb0C 1d2kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47661.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3)PLYSS / References: UniProt: Q873X9, chitinase #2: Chemical | ChemComp-SO4 / #3: 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: 3.59 Å3/Da / Density % sol: 65.73 % |
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Crystal grow | pH: 9.5 / Details: 1.4 M LI2SO4,0.1 M TRIS PH 9.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 23, 2003 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 147072 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D2K Resolution: 1.7→19.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2104628.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8801 Å2 / ksol: 0.34616 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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