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Yorodumi- PDB-1lf7: Crystal Structure of Human Complement Protein C8gamma at 1.2 A Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lf7 | ||||||
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Title | Crystal Structure of Human Complement Protein C8gamma at 1.2 A Resolution | ||||||
Components | Complement Protein C8gamma | ||||||
Keywords | IMMUNE SYSTEM / lipocalin / beta barrel / calyx / complement / MAC | ||||||
Function / homology | Function and homology information Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism / protein-containing complex binding / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.2 Å | ||||||
Authors | Ortlund, E. / Parker, C.L. / Schreck, S.F. / Ginell, S. / Minor, W. / Sodetz, J.M. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of human complement protein C8gamma at 1.2 A resolution reveals a lipocalin fold and a distinct ligand binding site. Authors: Ortlund, E. / Parker, C.L. / Schreck, S.F. / Ginell, S. / Minor, W. / Sodetz, J.M. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lf7.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lf7.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lf7 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lf7 | HTTPS FTP |
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-Related 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: 20305.979 Da / Num. of mol.: 1 / Mutation: C40G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: 9q34.3 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07360 |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
-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: 44.61 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 4000, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 26, 1999 |
Radiation | Monochromator: High resolution pass with 0.6 degree osc. Low resolution pass with 1.5 degree osc. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 57166 / Num. obs: 53030 / % possible obs: 92.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.2→1.24 Å / % possible all: 63.3 |
Reflection | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 63.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.2→36.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 364398.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with Turbo Frodo.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1352 Å2 / ksol: 0.371956 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→36.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.28 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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