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Yorodumi- PDB-1nr2: High resolution crystal structures of thymus and activation-regul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nr2 | ||||||
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Title | High resolution crystal structures of thymus and activation-regulated chemokine | ||||||
Components | Thymus and activation-regulated chemokine | ||||||
Keywords | CYTOKINE / TARC / chemokine / CC-chemokine / chemotaxis | ||||||
Function / homology | Function and homology information CCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of cell migration / inflammatory response ...CCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / positive regulation of cell migration / inflammatory response / signaling receptor binding / extracellular space / extracellular region Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Asojo, O.A. / Boulegue, C. / Hoover, D.M. / Lu, W. / Lubkowski, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structures of thymus and activation-regulated chemokine (TARC). Authors: Asojo, O.A. / Boulegue, C. / Hoover, D.M. / Lu, W. / Lubkowski, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and preliminary X-ray studies of thymus and activation-regulated chemokine Authors: Asojo, O.A. / Hoover, D. / Boulegue, C. / Cater, S. / Lu, W. / Lubkowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nr2.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nr2.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/1nr2 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nr2 | 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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Unit cell |
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-Components
#1: Protein | Mass: 8096.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q92583 #2: 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: 1.93 Å3/Da / Density % sol: 35.6 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.17M ammonium acetate, 0.085M trisodium citrate, 25.5% PEG 4000, 15% w/v glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 285 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2002 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→10 Å / Num. all: 6647 / Num. obs: 6647 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.064 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.194 / Rsym value: 0.271 / % possible all: 93.4 |
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 93.5 % / Redundancy: 5.5 % |
Reflection shell | *PLUS % possible obs: 92.2 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RANTES Resolution: 2.18→10 Å / Num. parameters: 4927 / Num. restraintsaints: 4188 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1231 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.198 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.18 Å / Lowest resolution: 2.26 Å / Rfactor Rfree: 0.391 / Rfactor Rwork: 0.26 |