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- PDB-9bex: X-ray crystallography structural model of the immunoglobulin G1 (... -

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Basic information

Entry
Database: PDB / ID: 9bex
TitleX-ray crystallography structural model of the immunoglobulin G1 (IgG1) Fc D270C K326C variant
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / antibody / crystallizable fragment / disulfide
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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsShenoy, A. / Barb, A.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01 AI148114 United States
CitationJournal: To Be Published
Title: X-ray crystallography structural model of the immunoglobulin G1 (IgG1) Fc D270C K326C variant
Authors: Shenoy, A. / Barb, A.W.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Immunoglobulin gamma-1 heavy chain
BBB: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5345
Polymers52,1772
Non-polymers3,3573
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.023, 79.740, 142.478
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: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 26088.605 Da / Num. of mol.: 2 / Mutation: D270C,K326C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#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)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH 7.5, 10% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30.502 Å / Num. obs: 46261 / % possible obs: 88.49 % / Redundancy: 2.2 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.07876 / Rpim(I) all: 0.06231 / Rrim(I) all: 0.101 / Net I/σ(I): 9.27
Reflection shellResolution: 2.25→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 3716 / CC1/2: 0.641 / CC star: 0.884 / Rpim(I) all: 0.3953 / Rrim(I) all: 0.5977 / % possible all: 52.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→30.502 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.243 / SU B: 9.984 / SU ML: 0.236 / Average fsc free: 0.8361 / Average fsc work: 0.8714 / Cross valid method: FREE R-VALUE / ESU R: 0.375 / ESU R Free: 0.285
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3017 1213 4.926 %
Rwork0.2422 23412 -
all0.245 --
obs-24625 88.411 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.285 Å2
Baniso -1Baniso -2Baniso -3
1--1.423 Å2-0 Å20 Å2
2--1.281 Å2-0 Å2
3---0.142 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 227 90 3674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133708
X-RAY DIFFRACTIONr_bond_other_d0.0180.0173240
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.7445086
X-RAY DIFFRACTIONr_angle_other_deg1.5771.6487633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46724.323155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90415552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.622159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
X-RAY DIFFRACTIONr_nbd_refined0.1990.2562
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.22817
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21700
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1080.21530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2770.211
X-RAY DIFFRACTIONr_nbd_other0.2750.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.360.22
X-RAY DIFFRACTIONr_mcbond_it3.5494.9761718
X-RAY DIFFRACTIONr_mcbond_other3.5474.9751717
X-RAY DIFFRACTIONr_mcangle_it5.4267.4462143
X-RAY DIFFRACTIONr_mcangle_other5.4267.4472144
X-RAY DIFFRACTIONr_scbond_it3.735.4271990
X-RAY DIFFRACTIONr_scbond_other3.7295.4291991
X-RAY DIFFRACTIONr_scangle_it5.5188.0252942
X-RAY DIFFRACTIONr_scangle_other5.5178.0272943
X-RAY DIFFRACTIONr_lrange_it8.04858.2083662
X-RAY DIFFRACTIONr_lrange_other8.04758.223656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3080.393340.3358640.33720090.7290.72844.69890.329
2.308-2.3710.423770.34313470.34819720.6940.72372.2110.323
2.371-2.4390.347820.30815260.3119100.8070.82784.18850.276
2.439-2.5140.377840.30416180.30718670.7650.81591.16230.271
2.514-2.5960.4091000.29315560.29917880.7610.82392.61750.258
2.596-2.6860.356640.27915670.28217510.8150.86793.14680.241
2.686-2.7870.363760.24614960.25117010.8350.89392.41620.216
2.787-2.8990.323820.25514240.25816090.850.88593.59850.226
2.899-3.0270.39810.25513850.26215680.7970.86593.49490.231
3.027-3.1730.368540.27113640.27515030.7910.84594.34460.253
3.173-3.3430.338680.27513080.27914390.8620.88795.6220.261
3.343-3.5430.296670.27312290.27413630.9030.92495.08440.27
3.543-3.7840.317550.27511740.27712870.8720.90395.49340.275
3.784-4.0820.314690.23510750.2411960.8910.92395.65220.236
4.082-4.4640.218500.18810330.1911220.9410.95296.52410.206
4.464-4.9770.176570.1579260.15810190.9640.96696.46710.177
4.977-5.7220.236310.1838380.1858940.9640.96897.20360.205
5.722-6.9470.37340.257390.2557880.9230.94698.09650.279
6.947-9.5790.24320.195850.1936360.9520.96197.01260.235
9.579-30.5020.302160.2793560.284090.9180.9390.95350.347

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