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Yorodumi- PDB-1tvx: NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tvx | ||||||
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Title | NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITIONAL AMINO TERMINAL RESIDUES (DSDLY) | ||||||
Components | NEUTROPHIL ACTIVATING PEPTIDE 2 VARIANT | ||||||
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 / tertiary granule lumen / Platelet degranulation / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Malkowski, M.G. / Edwards, B.F.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence. Authors: Malkowski, M.G. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F. #1: 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. #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. / Clore, G.M. / Gronenborn, A.M. / al., et #3: Journal: J.Biol.Chem. / Year: 1989 Title: The Three-Dimensional Structure of Bovine Platelet Factor 4 at 3.0-A Resolution Authors: Charles, R.St. / Walz, D.A. / Edwards, B.F. | ||||||
History |
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Remark 700 | SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL ...SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL MONOMERS. TWO MONOMERS COMBINE TO FORM AN EXTENDED SIX STRANDED BETA SHEET DIMER. TWO DIMERS ARE THEN ARRANGED BACK-TO-BACK TO FORM THE TETRAMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvx.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvx.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tvx_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 1tvx_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 1tvx_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1tvx_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvx ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvx | HTTPS FTP |
-Related structure data
Related structure data | 1napS 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: 8217.521 Da / Num. of mol.: 4 Mutation: M26L AND A FIVE RESIDUE (DSDLY) INSERT AT THE AMINO TERMINUS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02775 #2: Water | ChemComp-HOH / | Sequence details | THE NUMBERING SCHEME FOR ASP-CTAP FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE ...THE NUMBERING SCHEME FOR ASP-CTAP 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.6M CITRATE, 0.1M HEPES, PH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→9.6 Å / Num. obs: 25385 / % possible obs: 88 % / Observed criterion σ(I): 1 / Rsym value: 0.0388 |
Reflection | *PLUS Num. measured all: 50642 / Rmerge(I) obs: 0.039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NEUTROPHIL ACTIVATING PEPTIDE-2 (1NAP) Resolution: 1.75→7 Å
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Refinement step | Cycle: LAST / Resolution: 1.75→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 21058 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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