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Yorodumi- PDB-1nap: THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING ... -
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-Basic information
Entry | Database: PDB / ID: 1nap | ||||||
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Title | THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION | ||||||
Components | NEUTROPHIL ACTIVATING PEPTIDE-2 | ||||||
Keywords | CYTOKINE | ||||||
Function / homology | Function and homology information glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity ...glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Platelet degranulation / tertiary granule lumen / G alpha (i) signalling events / cellular response to lipopolysaccharide / defense response to bacterium / inflammatory response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Malkowski, M.G. / Edwards, B.F.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1995 Title: The crystal structure of recombinant human neutrophil-activating peptide-2 (M6L) at 1.9-A resolution. Authors: Malkowski, M.G. / Wu, J.Y. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F. #1: Journal: J.Biol.Chem. / Year: 1989 Title: The Three Dimensional Structure of Bovine Platelet Factor 4 at 3.0 Angstroms Resolution Authors: Charles, R.St. / Walz, D.A. / Edwards, B.F.P. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Crystal Structure of Interleukin 8: Symbiosis of NMR and Crystallography Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.C. / Appella, E. / Yamada, M. / Matsushima, K. / Edwards, B.F.P. / Clore, G.M. / Gronenborn, A.M. / Wlodawer, A. #3: Journal: Biochemistry / Year: 1990 Title: Three Dimensional Structure of Interleukin 8 in Solution Authors: Clore, G.M. / Appella, E. / Yamada, M. / Matsushima, K. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nap.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nap.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1nap ftp://data.pdbj.org/pub/pdb/validation_reports/na/1nap | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7623.935 Da / Num. of mol.: 4 / Mutation: M26L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBR-CRM-CTAP-MET20,LEU26 / Production host: Escherichia coli (E. coli) / References: UniProt: P02775 #2: Water | ChemComp-HOH / | Sequence details | THE NUMBERING SCHEME FOR NAP-2 FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES ...THE NUMBERING SCHEME FOR NAP-2 FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES IN BOVINE PLATELET FACTOR FOUR. THE NUMBERING SCHEME IS SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Num. obs: 17830 / % possible obs: 97 % / Num. measured all: 30511 / Rmerge(I) obs: 0.025 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 47 % |
-Processing
Software |
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Refinement | Resolution: 1.9→7 Å Details: THE MUTATION M26L IS DESCRIBED AS M6L IN THE JRNL REFERENCE.
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Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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