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- PDB-5dvm: Fc Design 20.8.37 B chain homodimer E357D/S364R/Y407A -

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Basic information

Entry
Database: PDB / ID: 5dvm
TitleFc Design 20.8.37 B chain homodimer E357D/S364R/Y407A
Components
  • Fc-III peptide
  • Ig gamma-1 chain C region
KeywordsIMMUNE SYSTEM / head-to-tail homodimer / Immunoglobulin / Fc
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 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 1.2Jul 6, 2016Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)27,1112
Polymers27,1112
Non-polymers00
Water1267
1
A: Ig gamma-1 chain C region
B: Fc-III peptide

A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)54,2224
Polymers54,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5250 Å2
ΔGint-39 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.197, 107.197, 56.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 25577.012 Da / Num. of mol.: 1 / Fragment: UNP residues 104-330 / Mutation: E357D, S364R, Y407A
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: Protein/peptide Fc-III peptide


Mass: 1533.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 100mM Sodium Cacodylate pH 6.5 + 20% PEG 8K + 200mM Magnesium Acetate tetrahydrate

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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: Jun 2, 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: 2.95→30 Å / Num. obs: 8056 / % possible obs: 98.7 % / Redundancy: 5.7 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Rsym value: 0.136 / Net I/av σ(I): 4.279 / Net I/σ(I): 7.9 / Num. measured all: 45883
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.95-3.1130.7961323510840.6310.7961.192.3
3.11-3.33.90.5091.5431210930.3280.5092.199.1
3.3-3.535.90.2922.5618210430.1350.2924.6100
3.53-3.816.80.2233.267449880.0920.2236.4100
3.81-4.176.80.1474.660028870.060.1479.4100
4.17-4.676.80.1115.356348340.0450.11112.399.9
4.67-5.396.70.115.447897190.0440.1113.6100
5.39-6.66.60.1085.441296230.0450.10813.5100
6.6-9.336.50.096.132214990.0370.0915.999.9
9.33-92.8355.70.0836.416352860.0370.08316.599.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0017refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
XDSdata reduction
RefinementResolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.583 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 370 4.6 %RANDOM
Rwork0.223 ---
obs0.2261 7658 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.5 Å2 / Biso mean: 69.424 Å2 / Biso min: 32.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å21.27 Å20 Å2
2--2.54 Å20 Å2
3----3.81 Å2
Refinement stepCycle: final / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 0 7 1701
Biso mean---51.33 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021746
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.9462396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.865218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59124.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66515257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.906156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221337
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 32 -
Rwork0.326 474 -
all-506 -
obs--86.79 %

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