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Yorodumi- PDB-1nwu: Crystal structure of human cartilage gp39 (HC-gp39) in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nwu | |||||||||
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Title | Crystal structure of human cartilage gp39 (HC-gp39) in complex with chitotetraose | |||||||||
Components | Chitinase-3 like protein 1 | |||||||||
Keywords | SIGNALING PROTEIN / chitinase-like protein / rheumatoid arthritis / chitin / N-acetylglucosamine | |||||||||
Function / homology | Function and homology information response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / cartilage development / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / cartilage development / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Fusetti, F. / Pijning, T. / Kalk, K.H. / Bos, E. / Dijkstra, B.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure and carbohydrate-binding properties of the human cartilage glycoprotein-39 Authors: Fusetti, F. / Pijning, T. / Kalk, K.H. / Bos, E. / Dijkstra, B.W. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS A1 ON SHEET RECORDS BELOW IS ACTUALLY AN ...SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS A1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS B1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS C1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS D1 ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED ALPHA/BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEETS A3A AND A3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS B3A AND B3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS C3A AND C3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). SHEETS D3A AND D3B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 11 AMINO ACIDS (RESIDUES 282-292) INCLUDES A HYDROGEN-BONDED TURN (RESIDUES 286-292). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nwu.cif.gz | 301.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nwu.ent.gz | 246.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nwu ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nwu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 40536.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: synovial cells, articular chondrocytes / Cell (production host): mammalian cho cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P36222 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.28 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 5.1 Details: PEG8000, NaCl, Na-citrate buffer, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.10 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 |
Detector | Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→41.99 Å / Num. obs: 107198 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.078 / Net I/σ(I): 18.5 |
Reflection shell | Highest resolution: 2.2 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.442 / % possible all: 99.2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. measured all: 572110 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.442 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3131745.66 / Data cutoff high rms absF: 3131745.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE IMPOSED ON THE FOLLOWING RESIDUE GROUPS IN ALL FOUR MOLECULES: GROUP 1: RESIDUES 22 TO 208, GROUP 2: RESIDUES 214 TO 226, GROUP 3: RESIDUES 235 ...Details: NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE IMPOSED ON THE FOLLOWING RESIDUE GROUPS IN ALL FOUR MOLECULES: GROUP 1: RESIDUES 22 TO 208, GROUP 2: RESIDUES 214 TO 226, GROUP 3: RESIDUES 235 TO 242, GROUP 4: RESIDUES 249 to 383
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.34 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→41.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. reflection obs: 107198 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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