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- PDB-1msb: STRUCTURE OF THE CALCIUM-DEPENDENT LECTIN DOMAIN FROM A RAT MANNO... -

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Basic information

Entry
Database: PDB / ID: 1msb
TitleSTRUCTURE OF THE CALCIUM-DEPENDENT LECTIN DOMAIN FROM A RAT MANNOSE-BINDING PROTEIN DETERMINED BY MAD PHASING
ComponentsMANNOSE-BINDING PROTEIN-A
KeywordsHEPATIC 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 / protein homotrimerization / D-mannose binding / polysaccharide 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 / protein homotrimerization / D-mannose binding / polysaccharide binding / complement activation, classical pathway / multivesicular body / positive regulation of phagocytosis / 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
Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
HOLMIUM ATOM / Mannose-binding protein A
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWeis, W.I. / Drickamer, K. / Hendrickson, W.A.
Citation
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.
#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.
History
DepositionSep 23, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNOSE-BINDING PROTEIN-A
B: MANNOSE-BINDING PROTEIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0366
Polymers25,3762
Non-polymers6604
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.400, 73.100, 45.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO A 186 AND PRO B 186 ARE CIS PROLINES.
2: THE FIRST TWO RESIDUES OF CHAIN A, THE FIRST THREE RESIDUES OF CHAIN B, AND THE LAST 2 RESIDUES OF CHAIN B ARE NOT WELL DEFINED.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.219746, -0.318844, 0.921982), (-0.260628, -0.929919, -0.25947), (0.940098, -0.183276, -0.287446)
Vector: -6.3206, 122.8365, 45.7491)

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Components

#1: Protein MANNOSE-BINDING PROTEIN-A


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: Chemical
ChemComp-HO / HOLMIUM ATOM


Mass: 164.930 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ho
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
210 mM1dropCaCl2
35 mM1dropNaCl
41.1 mM1dropMan6GlcNAc2Asn
515-20 %PEG33501reservoiror PEG8000
620 mM1reservoirCaCl2
7100 mMTris-HCl1reservoir
810 mM1reservoirNaCl
90.02 %1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 7195 / % possible obs: 89.3 % / Rmerge(I) obs: 0.031

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.176 / Highest resolution: 2.3 Å
Details: THE FIRST TWO RESIDUES OF CHAIN A, THE FIRST THREE RESIDUES OF CHAIN B, AND THE LAST 2 RESIDUES OF CHAIN B ARE NOT WELL DEFINED.
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 4 57 1839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.3 Å / Num. reflection all: 1839
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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