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Yorodumi- PDB-1h0g: Complex of a chitinase with the natural product cyclopentapeptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h0g | ||||||||||||||||||
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Title | Complex of a chitinase with the natural product cyclopentapeptide argadin from Clonostachys | ||||||||||||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / CHITIN DEGRADATION / ARGADIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||||||||||||||
Function / homology | Function and homology information chitinase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||||||||
Authors | Houston, D. / Shiomi, K. / Arai, N. / Omura, S. / Peter, M.G. / Turberg, A. / Synstad, B. / Eijsink, V.G.H. / Aalten, D.M.F. | ||||||||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: High Resolution Inhibited Complexes of a Chitinase with Natural Product Cyclopentapeptides - Peptide Mimicry of a Carbohydrate Substrate Authors: Houston, D.R. / Shiomi, K. / Arai, N. / Omura, S. / Peter, M.G. / Turberg, A. / Synstad, B. / Eijsink, V.G.H. / 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h0g.cif.gz | 221.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h0g.ent.gz | 176.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h0g ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h0g | HTTPS FTP |
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-Related structure data
Related structure data | 1h0iC 1e15S 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: 55548.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BOUND TO ARGADIN / Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11797, chitinase #2: Protein/peptide | #3: Chemical | ChemComp-GOL / #4: 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: 2.4 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 20% GLYCEROL 0.1M HEPES PH 7, 1.4M AMMONIUM SULPHATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging dropDetails: van Aalten, D.M.F., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.953758 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953758 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 69979 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. measured all: 224646 |
Reflection shell | *PLUS % possible obs: 93.3 % / Num. unique obs: 6563 / Num. measured obs: 18204 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+15 / Resolution: 2→29.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2862746.49 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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