+Open data
-Basic information
Entry | Database: PDB / ID: 3pog | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the MASP-1 CUB2 domain bound to Ca2+ | ||||||
Components | Mannan-binding lectin serine protease 1 | ||||||
Keywords | HYDROLASE / CUB domain / Ca2+ binding site / complement protein / lectin pathway of complement / MBL / MBP / ficolins / Bloodstream | ||||||
Function / homology | Function and homology information Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.749 Å | ||||||
Authors | Gingras, A.R. / Moody, P.C.E. / Wallis, R. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation. Authors: Gingras, A.R. / Girija, U.V. / Keeble, A.H. / Panchal, R. / Mitchell, D.A. / Moody, P.C. / Wallis, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pog.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pog.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3pog ftp://data.pdbj.org/pub/pdb/validation_reports/po/3pog | HTTPS FTP |
---|
-Related structure data
Related structure data | 3pobC 3podC 3poeSC 3pofC 3poiC 3pojC 3ponC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13091.511 Da / Num. of mol.: 3 / Fragment: MASP-1 CUB2 domain (UNP Residues 188-301) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Crarf, MASP-1/-3, Masp1, Masp3 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8CHN8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 24% PEG 8,000, 50mM Tris buffer, pH 9.0, 200mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2010 / Details: mirrors |
Radiation | Monochromator: optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.749→38.89 Å / Num. obs: 8258 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.26 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 5.81 |
Reflection shell | Resolution: 2.749→2.91 Å / Redundancy: 2.08 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.7 / % possible all: 78.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3POE Resolution: 2.749→38.98 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.822 / SU B: 13.232 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.999 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.749→38.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.749→2.82 Å / Total num. of bins used: 20
|