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- PDB-5dvo: Fc K392D/K409D homodimer -

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Basic information

Entry
Database: PDB / ID: 5dvo
TitleFc K392D/K409D homodimer
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / head-to-tail homodimer / Immunoglobulin / Fc
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
Model detailsDesign XXX
AuthorsAtwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. ...Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. / Fitchett, J.R. / Gutierrez, B. / Hendle, J. / Demarest, S.J. / Kuhlman, B.
CitationJournal: Structure / Year: 2016
Title: Computationally Designed Bispecific Antibodies using Negative State Repertoires.
Authors: Leaver-Fay, A. / Froning, K.J. / Atwell, S. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Hassanali, S. / Chamberlain, A.K. / Fitchett, J.R. / Demarest, S.J. / Kuhlman, B.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3624
Polymers51,1702
Non-polymers1922
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-42 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.657, 71.657, 100.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 25584.834 Da / Num. of mol.: 2 / Fragment: UNP residues 104-330 / Mutation: K392D, K409D
Source method: isolated from a genetically manipulated source
Details: transient expression / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 100mM Sodium Acetate pH 4.5 + 2000mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 25, 2014 / Details: Diamond (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17696 / % possible obs: 100 % / Redundancy: 7.7 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.172 / Rsym value: 0.151 / Net I/av σ(I): 4.222 / Net I/σ(I): 10.4 / Num. measured all: 136052
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.647.50.7720.91928025830.3260.7722.7100
2.64-2.87.80.5281.31877224220.2190.5283.9100
2.8-2.997.70.3542.11774822920.1460.3545.5100
2.99-3.237.80.2153.51655721310.0890.2158.3100
3.23-3.547.80.1294.71518219530.0530.12912.2100
3.54-3.957.80.1036.81383217840.0430.10314.2100
3.95-4.567.80.0837.61214115650.0340.08317.6100
4.56-5.597.70.1115.51030513390.0440.11118.7100
5.59-7.917.70.1025.5798710430.0410.10218.4100
7.91-50.6697.30.04510.842485840.020.04527.299.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0017refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementResolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.508 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 897 5.1 %RANDOM
Rwork0.1904 ---
obs0.1939 16769 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.22 Å2 / Biso mean: 32.178 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.38 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 10 142 3351
Biso mean--60.29 32.67 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023301
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.964522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41125.034145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8615497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.91510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222544
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 69 -
Rwork0.317 1224 -
all-1293 -
obs--99.92 %

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