[English] 日本語
Yorodumi- PDB-2msb: STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2msb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN OLIGOSACCHARIDE | |||||||||
Components | MANNOSE-BINDING PROTEIN-A | |||||||||
Keywords | LECTIN | |||||||||
Function / homology | Function and homology information 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 | Rattus rattus (black rat) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Weis, W.I. / Drickamer, K. / Hendrickson, W.A. | |||||||||
Citation | Journal: Nature / Year: 1992 Title: Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Authors: Weis, W.I. / Drickamer, K. / Hendrickson, W.A. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Physical Characterization and Crystallization of the Carbohydrate-Recognition Domain of a Mannose-Binding Protein from Rat Authors: Weis, W.I. / Crichlow, G.V. / Murthy, H.M.K. / Hendrickson, W.A. / Drickamer, K. #2: Journal: Science / Year: 1991 Title: Structure of the Calcium-Dependent Lectin Domain from a Rat Mannose-Binding Protein Determined by MAD Phasing Authors: Weis, W.I. / Kahn, R. / Fourme, R. / Drickamer, K. / Hendrickson, W.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2msb.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2msb.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 2msb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2msb_validation.pdf.gz | 840.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2msb_full_validation.pdf.gz | 840.7 KB | Display | |
Data in XML | 2msb_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2msb_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/2msb ftp://data.pdbj.org/pub/pdb/validation_reports/ms/2msb | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO A 186 AND PRO B 186 ARE CIS PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.21747, -0.34809, -0.91189), Vector: Details | THE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE DIMERIC PROTEIN MOLECULE (2 IDENTICAL CHAINS CORRESPONDING TO RESIDUES 107 - 221 MBP-A), AND ONE GLYCOPEPTIDE MOLECULE (6 MANNOSE, 2 GLCNAC (NAG), 1 ASN). FIVE OF THE MANNOSE RESIDUES CROSSLINK NEIGHBORING DIMERS OF THE CRYSTAL. MAN 9 BINDS TO CHAIN 2, AND MAN 8 BINDS TO THE (-X, Y + 1/2, 1 - Z) SYMMETRY MATE OF CHAIN 1. THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION WAS DERIVED BY LEAST-SQUARES SUPERPOSITION OF THE MAIN CHAIN N, CA, C, O AND CB, WHERE PRESENT, OF RESIDUES 110 - 220. | |
-Components
#1: Protein | Mass: 12688.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P19999 #2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 8 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. obs: 22750 / % possible obs: 91 % / Observed criterion σ(I): 3 / Num. measured all: 17511 / Rmerge(I) obs: 0.07 |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→10 Å / σ(F): 3 Details: AN OVERALL ANISOTROPIC TEMPERATURE FACTOR IS REQUIRED TO CORRECTLY MODEL THE DATA, BUT HAS NOT BEEN APPLIED TO THE SUBMITTED MODEL (OR STRUCTURE FACTORS). THE VALUES OF THE TENSOR ARE: B(11) ...Details: AN OVERALL ANISOTROPIC TEMPERATURE FACTOR IS REQUIRED TO CORRECTLY MODEL THE DATA, BUT HAS NOT BEEN APPLIED TO THE SUBMITTED MODEL (OR STRUCTURE FACTORS). THE VALUES OF THE TENSOR ARE: B(11) = 4.1 ANGSTROMS**2 B(12) = B(23) = 0.0 ANGSTROMS**2 B(13) = 2.2 ANGSTROMS**2 B(22) = -4.0 ANGSTROMS**2 B(33) = -4.2 ANGSTROMS**2 THE TENSOR IS DEFINED IN SHERIFF, S. AND HENDRICKSON, W.A. (1987) ACTA CRYST. A43:118-121.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 20461 / σ(F): 3 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|