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- PDB-2msb: STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN O... -

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Basic information

Entry
Database: PDB / ID: 2msb
TitleSTRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN OLIGOSACCHARIDE
ComponentsMANNOSE-BINDING PROTEIN-A
KeywordsLECTIN
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
Mannose-binding protein A
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWeis, 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
DepositionJul 28, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,8119
Polymers25,3762
Non-polymers1,4357
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.810, 85.160, 39.550
Angle α, β, γ (deg.)90.00, 97.41, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: 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), (-0.33364, -0.90448, 0.2657), (-0.91727, 0.24646, -0.31284)
Vector: 16.1798, 0.2936, 21.6342)
DetailsTHE 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.

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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: 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


Type: oligosaccharide / Mass: 1194.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-3-3-3/a4-b1_b3-c1_b6-e1_c2-d1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp6Me]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
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

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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 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.
RfactorNum. reflection
Rwork0.174 -
obs0.174 20461
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 64 211 2016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
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: 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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.4
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it1.7
X-RAY DIFFRACTIONx_scangle_it2.8

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