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- PDB-2brs: EMBP Heparin complex -

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Basic information

Entry
Database: PDB / ID: 2brs
TitleEMBP Heparin complex
ComponentsEOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
KeywordsLECTIN / ANTIBIOTIC / EMBP / EOSINOPHIL / EOSINOPHIL GRANULE PROTEIN / GLYCOPROTEIN / HEPARIN-BINDING / IMMUNE RESPONSE / PROTEOGLYCAN / HEPARIN
Function / homology
Function and homology information


extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen ...extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / defense response to bacterium / immune response / Neutrophil degranulation / extracellular exosome / extracellular region
Similarity search - Function
Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / 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) ...Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / 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
Bone marrow proteoglycan
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSwaminathan, G.J. / Myszka, D.G. / Katsamba, P.S. / Ohnuki, L.E. / Gleich, G.J. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 2005
Title: Eosinophil-Granule Major Basic Protein, a C-Type Lectin, Binds Heparin
Authors: Swaminathan, G.J. / Myszka, D.G. / Katsamba, P.S. / Ohnuki, L.E. / Gleich, G.J. / Acharya, K.R.
History
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
B: EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,00611
Polymers27,6422
Non-polymers1,3649
Water1,65792
1
A: EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8977
Polymers13,8211
Non-polymers1,0766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1094
Polymers13,8211
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.913, 57.917, 61.831
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7405, 0.04083, 0.67081), (0.03493, -0.99914, 0.02226), (0.67115, 0.00695, -0.74129)
Vector: -19.47929, 73.52886, 48.33795)

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Components

#1: Protein EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN / MBP / EMBP / PREGNANCY ASSOCIATED MAJOR BASIC PROTEIN / PROTEOGLYCAN 2 BONE MARROW / BMPG


Mass: 13820.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HEPARIN SULPHATE / Source: (natural) HOMO SAPIENS (human) / Cell: EOSINOPHIL / References: UniProt: P13727
#2: Polysaccharide 2-O-sulfo-beta-L-altropyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 595.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2111A-1b_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][b-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: IT IS A CYTOTOXIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.58 %

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.449
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.449 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 12698 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8U

1h8u


Resolution: 2.2→35.23 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1525227.49 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 632 5 %RANDOM
Rwork0.247 ---
obs0.247 12698 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.024 Å2 / ksol: 0.400786 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-19.93 Å20 Å28.15 Å2
2---13.41 Å20 Å2
3----6.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 75 92 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.42
X-RAY DIFFRACTIONc_scangle_it2.162.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 119 5.8 %
Rwork0.343 1943 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4IDU.PARIDU.TOP
X-RAY DIFFRACTION5SGN.PARSGN.TOP

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