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- PDB-1ayo: RECEPTOR BINDING DOMAIN OF BOVINE ALPHA-2-MACROGLOBULIN -

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Basic information

Entry
Database: PDB / ID: 1ayo
TitleRECEPTOR BINDING DOMAIN OF BOVINE ALPHA-2-MACROGLOBULIN
ComponentsALPHA-2-MACROGLOBULIN
KeywordsMACROGLOBULIN / RECEPTOR BINDING DOMAIN
Function / homology
Function and homology information


negative regulation of complement activation, lectin pathway / interleukin-1 binding / brain-derived neurotrophic factor binding / interleukin-8 binding / response to prostaglandin E / embryonic liver development / acute inflammatory response to antigenic stimulus / luteinization / tumor necrosis factor binding / HDL assembly ...negative regulation of complement activation, lectin pathway / interleukin-1 binding / brain-derived neurotrophic factor binding / interleukin-8 binding / response to prostaglandin E / embryonic liver development / acute inflammatory response to antigenic stimulus / luteinization / tumor necrosis factor binding / HDL assembly / response to carbon dioxide / nerve growth factor binding / endopeptidase inhibitor activity / growth factor binding / response to glucocorticoid / Intrinsic Pathway of Fibrin Clot Formation / Degradation of the extracellular matrix / response to nutrient / platelet alpha granule lumen / acute-phase response / stem cell differentiation / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / Platelet degranulation / collagen-containing extracellular matrix / protease binding / blood microparticle / signaling receptor binding / enzyme binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Alpha-macroglobulin, receptor-binding domain / Alpha-2-macroglobulin, TED domain / TonB box, conserved site / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 ...Alpha-macroglobulin, receptor-binding domain / Alpha-2-macroglobulin, TED domain / TonB box, conserved site / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-2-macroglobulin / Alpha-2-macroglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsJenner, L.B. / Husted, L. / Thirup, S. / Sottrup-Jensen, L. / Nyborg, J.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of the receptor-binding domain of alpha 2-macroglobulin.
Authors: Jenner, L. / Husted, L. / Thirup, S. / Sottrup-Jensen, L. / Nyborg, J.
History
DepositionNov 7, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: 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: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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.ptnr1_symmetry / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-2-MACROGLOBULIN
B: ALPHA-2-MACROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4764
Polymers29,0112
Non-polymers4642
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.570, 107.570, 72.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ALPHA-2-MACROGLOBULIN


Mass: 14505.549 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN / Source method: isolated from a natural source / Details: N-LINKED GLYCOSYLATION SITE ON ASN B 68 / Source: (natural) Bos taurus (cattle) / Tissue: PLASMA / References: UniProt: P01023, UniProt: Q7SIH1*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Description: DATA WERE COLLECTED AT THE X-RAY DIFFRACTION BEAMLINE IN TRIESTE, ITALY.
Crystal growpH: 6.9
Details: 38% PEGMMES 2000, 25 MM CACL2, 100 MM HEPES, PH 6.9
Crystal grow
*PLUS
Method: batch method / PH range low: 7.4 / PH range high: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 %(w/v)mPEG200011
2100 mMHEPES11titrated with NaOH
320 mM11CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 1, 1997 / Details: DUEL SLITS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→33 Å / Num. obs: 35602 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 23
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.265 / % possible all: 82.6
Reflection
*PLUS
Num. obs: 35876 / % possible obs: 91 % / Num. measured all: 453466 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 82.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→33 Å / Num. parameters: 9496 / Num. restraintsaints: 8488 / Cross valid method: FREE R-VALUE / σ(F): 0 / StereochEM target val spec case: NAG / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995)53-56.
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1032 3 %THIN SHELLS
all0.1973 35876 --
obs0.1947 -91 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. (1973) 91: 201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2370
Refinement stepCycle: LAST / Resolution: 1.9→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 29 304 2370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.092
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.619

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