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Yorodumi- PDB-1rs0: Crystal Structure Analysis of the Bb segment of Factor B complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rs0 | ||||||
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Title | Crystal Structure Analysis of the Bb segment of Factor B complexed with Di-isopropyl-phosphate (DIP) | ||||||
Components | Complement factor B | ||||||
Keywords | HYDROLASE / factor B / Bb / factor Bb-DIP complex | ||||||
Function / homology | Function and homology information alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ponnuraj, K. / Xu, Y. / Macon, K. / Moore, D. / Volanakis, J.E. / Narayana, S.V. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structural analysis of engineered Bb fragment of complement factor B: insights into the activation mechanism of the alternative pathway C3-convertase. Authors: Ponnuraj, K. / Xu, Y. / Macon, K. / Moore, D. / Volanakis, J.E. / Narayana, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rs0.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rs0.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rs0_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 1rs0_full_validation.pdf.gz | 462.5 KB | Display | |
Data in XML | 1rs0_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1rs0_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/1rs0 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/1rs0 | HTTPS FTP |
-Related structure data
Related structure data | 1rrkSC 1rtkC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56246.160 Da / Num. of mol.: 1 / Fragment: COMPLEMENT FACTOR B BB FRAGMENT / Mutation: F428C, N435C, C267V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: SF9 cells were also used / Gene: BF / Cell (production host): egg / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase |
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-Non-polymers , 5 types, 209 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-DFP / | #6: 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: 3.13 Å3/Da / Density % sol: 60.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEGMME 2000, NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 21316 / Num. obs: 21183 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.036 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRK Resolution: 2.6→19.82 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 160612.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.4137 Å2 / ksol: 0.340998 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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