+Open data
-Basic information
Entry | Database: PDB / ID: 1d9c | ||||||
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Title | BOVINE INTERFERON-GAMMA AT 2.0 ANGSTROMS | ||||||
Components | INTERFERON-GAMMA | ||||||
Keywords | IMMUNE SYSTEM / helical homodimer | ||||||
Function / homology | Function and homology information Interferon gamma signaling / Regulation of IFNG signaling / IFNG signaling activates MAPKs / type II interferon receptor binding / humoral immune response / positive regulation of B cell proliferation / cytokine activity / defense response to virus / adaptive immune response / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Randal, M. / Kossiakoff, A.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. Authors: Randal, M. / Kossiakoff, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d9c.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9c.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d9c_validation.pdf.gz | 365.5 KB | Display | wwPDB validaton report |
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Full document | 1d9c_full_validation.pdf.gz | 369.7 KB | Display | |
Data in XML | 1d9c_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1d9c_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9c ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the asymmetric unit contains the biologically relevant homodimer |
-Components
#1: Protein | Mass: 14255.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P07353 #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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, sodium chloride, sodium citrate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal | *PLUS Density % sol: 39 % |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 50 %sat / Common name: sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→27 Å / Num. all: 16274 / Num. obs: 71885 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 72.5 |
Reflection shell | Resolution: 2.02→2.07 Å / % possible all: 86.5 |
Reflection | *PLUS Num. obs: 16274 / Num. measured all: 71855 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
Software |
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Refinement | Resolution: 2→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 349992.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: NCS restraints were applied to individual helices, BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: flat model / Bsol: 63.9842 Å2 / ksol: 0.341298 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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