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- PDB-6bhq: Mouse Immunoglobulin G 2c Fc fragment with complex-type glycan -

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Basic information

Entry
Database: PDB / ID: 6bhq
TitleMouse Immunoglobulin G 2c Fc fragment with complex-type glycan
ComponentsIgh protein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFalconer, D. / Barb, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115489 United States
CitationJournal: PLoS ONE / Year: 2018
Title: Mouse IgG2c Fc loop residues promote greater receptor-binding affinity than mouse IgG2b or human IgG1.
Authors: Falconer, D.J. / Barb, A.W.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Igh protein
B: Igh protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9845
Polymers50,0472
Non-polymers2,9373
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint39 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.735, 73.399, 118.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Igh protein


Mass: 25023.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh / Production host: Homo sapiens (human) / References: UniProt: Q58E56
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50 mM HEPES, 5% PEG 3.35K, pH 7.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→46.08 Å / Num. obs: 37350 / % possible obs: 99 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.052 / Net I/σ(I): 16.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.489 / Num. unique obs: 3533 / CC1/2: 0.81 / Rrim(I) all: 0.553 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rgs

2rgs


Resolution: 2.05→46.082 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 3698 9.9 %
Rwork0.2371 --
obs0.2392 37347 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→46.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 198 193 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023455
X-RAY DIFFRACTIONf_angle_d2.0924736
X-RAY DIFFRACTIONf_dihedral_angle_d22.4151303
X-RAY DIFFRACTIONf_chiral_restr0.132590
X-RAY DIFFRACTIONf_plane_restr0.012568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.0770.35281250.34611177X-RAY DIFFRACTION93
2.077-2.10540.32981340.33751245X-RAY DIFFRACTION96
2.1054-2.13550.30831170.31131257X-RAY DIFFRACTION98
2.1355-2.16740.31341430.30321300X-RAY DIFFRACTION99
2.1674-2.20120.32341600.30891247X-RAY DIFFRACTION99
2.2012-2.23730.33831670.30711261X-RAY DIFFRACTION100
2.2373-2.27590.31651430.29521309X-RAY DIFFRACTION100
2.2759-2.31730.29761520.28891264X-RAY DIFFRACTION100
2.3173-2.36190.28961360.31291293X-RAY DIFFRACTION100
2.3619-2.41010.32511390.31371285X-RAY DIFFRACTION100
2.4101-2.46250.3171290.29811299X-RAY DIFFRACTION99
2.4625-2.51980.32511310.29491290X-RAY DIFFRACTION98
2.5198-2.58280.31731390.29751279X-RAY DIFFRACTION99
2.5828-2.65260.31171130.28881307X-RAY DIFFRACTION100
2.6526-2.73060.33681710.28331298X-RAY DIFFRACTION100
2.7306-2.81880.30711510.26611279X-RAY DIFFRACTION99
2.8188-2.91950.31481640.27981261X-RAY DIFFRACTION99
2.9195-3.03640.29761490.27991306X-RAY DIFFRACTION100
3.0364-3.17450.26331370.24811309X-RAY DIFFRACTION100
3.1745-3.34180.25671420.23661307X-RAY DIFFRACTION99
3.3418-3.55110.2581350.23151313X-RAY DIFFRACTION100
3.5511-3.82520.23471550.21461303X-RAY DIFFRACTION100
3.8252-4.20990.22931080.19581363X-RAY DIFFRACTION99
4.2099-4.81850.17511490.17771338X-RAY DIFFRACTION100
4.8185-6.06870.22461570.17991346X-RAY DIFFRACTION100
6.0687-46.09330.22171520.21431413X-RAY DIFFRACTION98

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