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Open data
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Basic information
Entry | Database: PDB / ID: 1buu | ||||||
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Title | ONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A | ||||||
![]() | PROTEIN (MANNOSE-BINDING PROTEIN A) | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / HOST DEFENSE / METALLOPROTEIN | ||||||
Function / homology | ![]() calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / D-mannose binding ...calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / D-mannose binding / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / calcium ion binding / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ng, K.K.-S. / Park-Snyder, S. / Weis, W.I. | ||||||
![]() | ![]() Title: Ca2+-dependent structural changes in C-type mannose-binding proteins. Authors: Ng, K.K. / Park-Snyder, S. / Weis, W.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.5 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bv4C ![]() 1rtmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18449.816 Da / Num. of mol.: 1 Fragment: LECTIN, TRIMERIZATION, AND PORTION OF COLLAGENOUS DOMAIN DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HO / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST 4 RESIDUES IN THE EXPRESSION CONSTRUCT, ALA-ILE-GLU-VAL, ARE A CLONING ARTIFACT AND ARE ...THE FIRST 4 RESIDUES IN THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIR CONTAINING 11-15% (W/V) PEG 3350, 0.325 MM HOCL3, 100 MM TRIS-CL PH 8.0, 10 MM NACL, 0.02% NAN3., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 1994 / Details: 0.3 MM COLLIMATOR |
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: 1.9→50 Å / Num. obs: 20530 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.215 / Rsym value: 0.215 / % possible all: 88 |
Reflection shell | *PLUS % possible obs: 88 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RTM, CHAIN 1 Resolution: 1.9→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: MLF TARGET USED. THE FIRST 19 RESIDUES OF THE EXPRESSION CONSTRUCT, CONTAINING SEQUENCE FROM THE COLLAGENOUS DOMAIN, ARE DISORDERED AND CANNOT BE DISTINGUISHED IN ELECTRON DENSITY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.9 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.233 / Rfactor obs: 0.233 |