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- PDB-1w9v: Specificity and affinity of natural product cyclopentapeptide arg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w9v | ||||||
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Title | Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus fumigatus | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / CHITINASE / ARGIFIN / CHITINASE INHIBITORS / CYCLOPENTAPEPTIDE INHIBITORS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() chitinase / chitinase activity / chitin catabolic process / chitin binding / glycosyltransferase activity / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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. 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 | ![]() | 194.1 KB | Display | ![]() |
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PDB format | ![]() | 151.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1w9pC ![]() 1w9uC ![]() 1wawC ![]() 1wb0C ![]() 1d2kS 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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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.) ![]() ![]() ![]() ![]() References: UniProt: Q873X9, UniProt: E9QRF2*PLUS, chitinase #2: Protein/peptide | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.07 % |
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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: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEACH / Detector: CCD / Date: Nov 23, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979488 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 88304 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 79.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1D2K Resolution: 2→19.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2206999.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.65 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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