+Open data
-Basic information
Entry | Database: PDB / ID: 5fcr | ||||||
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Title | MOUSE COMPLEMENT FACTOR D | ||||||
Components | Complement factor D | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Alternative complement activation / complement factor D / Platelet degranulation / complement activation, alternative pathway / Notch signaling pathway / Neutrophil degranulation / response to bacterium / endopeptidase activity / serine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Mac Sweeney, A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Small-molecule factor D inhibitors targeting the alternative complement pathway. Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. ...Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. / Dussauge, S. / Hughes, N. / Delgado, O. / Hommel, U. / Gould, T. / Mac Sweeney, A. / Gerhartz, B. / Cumin, F. / Flohr, S. / Schubart, A. / Jaffee, B. / Harrison, R. / Risitano, A.M. / Eder, J. / Anderson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fcr.cif.gz | 400.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fcr.ent.gz | 326.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fcr_validation.pdf.gz | 496.3 KB | Display | wwPDB validaton report |
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Full document | 5fcr_full_validation.pdf.gz | 525.1 KB | Display | |
Data in XML | 5fcr_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 5fcr_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fcr ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fcr | HTTPS FTP |
-Related structure data
Related structure data | 5fahC 5fbeC 5fbiC 5fckSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25486.682 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cfd, Adn, Df / Production host: Escherichia coli (E. coli) / References: UniProt: P03953, complement factor D |
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-Non-polymers , 5 types, 846 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Mouse FD was crystallized by the sitting drop vapour diffusion method. A 1 uL FD solution (14.4 mg/mL FD, 50 mM Tris pH 8.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (0.1 M HEPES ...Details: Mouse FD was crystallized by the sitting drop vapour diffusion method. A 1 uL FD solution (14.4 mg/mL FD, 50 mM Tris pH 8.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0) and equilibrated against 200 uL reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→88.35 Å / Num. obs: 215515 / % possible obs: 88.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.72 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FCK Resolution: 1.25→83.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.308 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.735 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→83.45 Å
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Refine LS restraints |
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