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- PDB-6ka7: The complex structure of Human IgG Fc and its binding Repebody -

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Basic information

Entry
Database: PDB / ID: 6ka7
TitleThe complex structure of Human IgG Fc and its binding Repebody
Components
  • Immunoglobulin gamma-1 heavy chain
  • repebody
KeywordsIMMUNE SYSTEM / antibody / Fc / repebody
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChoi, J. / Kim, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education (Korea)2017R1A6A3A04012313 Korea, Republic Of
CitationJournal: To Be Published
Title: The complex structure of Human IgG Fc and its binding Repebody
Authors: Choi, J.
History
DepositionJun 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: repebody
B: repebody
C: Immunoglobulin gamma-1 heavy chain
D: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3996
Polymers104,4724
Non-polymers2,9272
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint46 kcal/mol
Surface area38330 Å2
Unit cell
Length a, b, c (Å)59.926, 107.420, 171.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein repebody


Mass: 28561.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23674.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DOX5
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris HCl, PEG 4000, Sodium chloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 23908 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 62.08 Å2 / Rmerge(I) obs: 0.249 / Χ2: 1.965 / Net I/σ(I): 4.4 / Num. measured all: 316090
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
3-3.0512.611991.2541100
3.05-3.1112.811571.31100
3.11-3.1712.911561.331100
3.17-3.2312.811941.3591100
3.23-3.31311611.38311000.883
3.3-3.3813.111771.43111000.723
3.38-3.4613.211831.43611000.698
3.46-3.5613.411691.53411000.579
3.56-3.6613.411931.56511000.457
3.66-3.7813.611661.67911000.397
3.78-3.9113.711781.73311000.365
3.91-4.0713.911931.82211000.311
4.07-4.2513.911842.0311000.262
4.25-4.4813.911932.311000.224
4.48-4.7613.912132.46711000.21
4.76-5.1213.811992.51511000.186
5.12-5.6413.712032.5911000.181
5.64-6.4413.612232.46211000.183
6.44-8.0913.112382.96511000.146
8.09-3010.313294.135199.80.085

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.235 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.76
RfactorNum. reflection% reflection
Rfree0.3331 1142 5 %
Rwork0.2573 --
obs0.2611 22835 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.92 Å2 / Biso mean: 57.4629 Å2 / Biso min: 16.5 Å2
Refinement stepCycle: final / Resolution: 3→29.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 198 6 6718
Biso mean--76.43 35.2 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016876
X-RAY DIFFRACTIONf_angle_d1.2469435
X-RAY DIFFRACTIONf_chiral_restr0.0641150
X-RAY DIFFRACTIONf_plane_restr0.0071188
X-RAY DIFFRACTIONf_dihedral_angle_d4.2513973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0001-3.13650.48131390.355626412780
3.1365-3.30160.40641400.316326722812
3.3016-3.50810.38041420.284726842826
3.5081-3.77850.35511400.259926602800
3.7785-4.15780.37321420.244826962838
4.1578-4.75720.29621430.219627252868
4.7572-5.98510.26561450.245327572902
5.9851-29.23590.30091510.245828583009

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