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Yorodumi- PDB-1gpf: CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gpf | ||||||
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Title | CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN | ||||||
Components | CHITINASE B | ||||||
Keywords | HYDROLASE / CHITIN DEGRADATION / INHIBITOR PSAMMAPLIN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Komander, D. / Van Aalten, D.M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2002 Title: Psammaplin A, a Chitinase Inhibitor Isolated from the Fijian Marine Sponge Aplysinella Rhax Authors: Tabudravu, J.N. / Eijsink, V.G. / Gooday, G.W. / Jaspars, M. / Komander, D. / Legg, M. / Synstad, B. / Van Aalten, D.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpf.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpf.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gpf_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 1gpf_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1gpf_validation.xml.gz | 42 KB | Display | |
Data in CIF | 1gpf_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpf ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpf | HTTPS FTP |
-Related structure data
Related structure data | 1e15S 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) / References: UniProt: Q54276, chitinase #2: Chemical | #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: 2.5 Å3/Da / Density % sol: 49.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 Details: 2.0M AMMONIUM SULFATE, 20% GLYCEROL, HEPES PH7.0, pH 7.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging dropDetails: van Aalten, D.M., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. obs: 254155 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 69.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 83126 / Num. measured all: 254155 |
Reflection shell | *PLUS % possible obs: 69.2 % / Num. unique obs: 6368 / Rmerge(I) obs: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E15 Resolution: 1.85→29.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2795287.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.2425 Å2 / ksol: 0.364016 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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