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Yorodumi- PDB-1hkm: High resolution crystal structure of human chitinase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hkm | |||||||||
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Title | High resolution crystal structure of human chitinase in complex with demethylallosamidin | |||||||||
Components | CHITOTRIOSIDASE | |||||||||
Keywords | HYDROLASE / HUMAN CHITINASE / CHITIN DEGRADATION / DEMETHYLALLOSAMIDIN | |||||||||
Function / homology | Function and homology information endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å | |||||||||
Authors | Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Sakuda, S. / Van Aalten, D.M.F. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase Authors: Rao, F.V. / Houston, D.R. / Boot, R.G. / Aerts, J.M.F.G. / Sakuda, 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 SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hkm.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hkm.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 1hkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hkm_validation.pdf.gz | 745.6 KB | Display | wwPDB validaton report |
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Full document | 1hkm_full_validation.pdf.gz | 754 KB | Display | |
Data in XML | 1hkm_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1hkm_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hkm ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hkm | HTTPS FTP |
-Related structure data
Related structure data | 1hkiC 1hkjC 1hkkC 1guvS 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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Unit cell |
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-Components
#1: Protein | Mass: 40783.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GLUCOSE ALLOSAMIDIN B / Source: (natural) HOMO SAPIENS (human) / Cell: MACROPHAGES / References: UniProt: Q13231, chitinase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ALI / |
#4: Water | ChemComp-HOH / |
-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: 48 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 25 % PEG 550 MME 0.01 M ZNSO4, 0.1 M MES PH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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: ID14-2 / Wavelength: 0.933 |
Detector | Detector: CCD / Date: Apr 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→25 Å / Num. obs: 13215 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2.55 Å / Lowest resolution: 25 Å / Redundancy: 4.8 % / Num. measured all: 63006 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 98.9 % / Redundancy: 4.8 % / Num. unique obs: 1283 / Num. measured obs: 6132 / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1GUV Resolution: 2.55→24.93 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1701806.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3798 Å2 / ksol: 0.345866 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→24.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.64 Å |