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- PDB-1afb: STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS -

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Basic information

Entry
Database: PDB / ID: 1afb
TitleSTRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS
ComponentsMANNOSE-BINDING PROTEIN-A
KeywordsLECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN
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
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 ...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
2-acetamido-2-deoxy-beta-D-galactopyranose / Mannose-binding protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKolatkar, A.R. / Weis, W.I.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Structural basis of galactose recognition by C-type animal lectins.
Authors: Kolatkar, A.R. / Weis, W.I.
#1: Journal: Structure / Year: 1994
Title: Trimeric Structure of a C-Type Mannose-Binding Protein
Authors: Weis, W.I. / Drickamer, K.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Binding of Sugar Ligands to Ca+2-Dependent Animal Lectins II. Generation of High-Affinity Galactose Binding by Site-Directed Mutagenesis
Authors: Iobst, S.T. / Drickamer, K.
History
DepositionNov 3, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: MANNOSE-BINDING PROTEIN-A
2: MANNOSE-BINDING PROTEIN-A
3: MANNOSE-BINDING PROTEIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17117
Polymers51,0763
Non-polymers1,09514
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-155 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.800, 84.500, 97.100
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 1 186 / 2: CIS PROLINE - PRO 2 186 / 3: CIS PROLINE - PRO 3 186
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.524376, -0.490972, -0.695684), (0.499408, -0.484403, 0.718294), (-0.689653, -0.724086, -0.008814)37.204, 5.136, 54.557
2given(0.463774, 0.513684, -0.721832), (-0.516961, -0.50476, -0.691352), (-0.719489, 0.693791, 0.03146)16.782, 60.142, 22.453
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 2 73 .. 2 226 1 73 .. 1 226 0.679 M2 3 73 .. 3 226 1 73 .. 1 226 0.329 THE TRANSFORMATIONS WERE DERIVED BY LEAST-SQUARES SUPERPOSITION OF THE MAIN CHAIN N, CA, C, O, CB, WHERE PRESENT, OF RESIDUES 73 TO 226.

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Components

#1: Protein MANNOSE-BINDING PROTEIN-A / CL-QPDWG


Mass: 17025.295 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Mutation: E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196)
Source method: isolated from a genetically manipulated source
Details: PH 8.0, DATA COLLECTED AT 100K, 20% 2-METHYL,2-4 PENTANEDIOL (CRYOPROTECTANT)
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: THE BACTERIALLY EXPRESSED MATERIAL IS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS
Plasmid: PINIIIOMPA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19999
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS AN INSERTION AFTER RESIDUE SER 191. RESIDUES ARE NUMBERED CONSECUTIVELY THEREAFTER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Density % sol: 68 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
210 mM1dropCaCl2
310 mM1dropNaCl
420 %MPD1drop
512-15 %PEG80001reservoir
6100 mMTris-HCl1reservoir
720 mM1reservoirCaCl2
80.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 47904 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.046
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 85 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.223

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3model building
X-PLOR3.54refinement
X-PLOR3phasing
RefinementResolution: 1.9→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.261 -10.2 %
Rwork0.217 --
obs0.217 43050 93.5 %
Displacement parametersBiso mean: 31.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 56 371 4017
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11
X-RAY DIFFRACTIONx_mcangle_it1.22
X-RAY DIFFRACTIONx_scbond_it2.31.5
X-RAY DIFFRACTIONx_scangle_it2.72.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 47904
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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