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Yorodumi- PDB-4cbo: Crystal structure of Complement Factor D mutant R202A after ensem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbo | ||||||
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Title | Crystal structure of Complement Factor D mutant R202A after ensemble refinement | ||||||
Components | COMPLEMENT FACTOR D | ||||||
Keywords | HYDROLASE / FACTOR D / ENSEMBLE REFINEMENT | ||||||
Function / homology | Function and homology information complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Forneris, F. / Burnley, B.T. / Gros, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Ensemble Refinement Shows Conformational Flexibility in Crystal Structures of Human Complement Factor D Authors: Forneris, F. / Burnley, B.T. / Gros, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cbo.cif.gz | 24.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbo.ent.gz | 21.2 MB | Display | PDB format |
PDBx/mmJSON format | 4cbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cbo_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 4cbo_full_validation.pdf.gz | 862.5 KB | Display | |
Data in XML | 4cbo_validation.xml.gz | 601.1 KB | Display | |
Data in CIF | 4cbo_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbo ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbo | HTTPS FTP |
-Related structure data
Related structure data | 4cbnC 1dsuS C: citing same article (ref.) 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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2 |
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Unit cell |
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Number of models | 77 |
-Components
#1: Protein | Mass: 24352.691 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-253 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P00746, complement factor D #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | MUTATION R202A | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | Details: 15% PEG 6000, 50 MM MES/NAOH PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.33 Å / Num. obs: 37211 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DSU Resolution: 1.8→47.332 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 19.77 / Stereochemistry target values: ML / Details: NUMBER OF STRUCTURES IN THE ENSEMBLE IS 77
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.332 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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