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- PDB-5dvk: Fc Design 7.7 B chain homodimer T366V/K409I -

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Basic information

Entry
Database: PDB / ID: 5dvk
TitleFc Design 7.7 B chain homodimer T366V/K409I
Components(Ig gamma-1 chain C region) x 2
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: 2.6 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

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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: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)27,1292
Polymers27,1292
Non-polymers00
Water905
1
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region

A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)54,2584
Polymers54,2584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5430 Å2
ΔGint-37 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.870, 107.870, 56.632
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: 25595.023 Da / Num. of mol.: 1 / Fragment: UNP residues 104-330 / Mutation: T366V, K409I
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 Ig gamma-1 chain C region


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 100mM Hepes pH 7.5 + 10% Isopropanol + 20% PEG 4K

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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 21, 2014 / Details: Diamond (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979311
ReflectionResolution: 2.6→30 Å / Num. obs: 11789 / % possible obs: 98.9 % / Redundancy: 11 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.127 / Rsym value: 0.117 / Net I/av σ(I): 4.751 / Net I/σ(I): 13.5 / Num. measured all: 129162
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
2.6-2.749.60.8030.91518115830.280.8032.793.7
2.74-2.9111.30.571.31844116320.1840.574.499.8
2.91-3.1111.30.3072.51725315220.0980.3077.599.8
3.11-3.3611.30.1754.21623814370.0560.17511.599.8
3.36-3.6811.30.11561478913080.0370.11516.199.9
3.68-4.1111.20.0927.11356812080.0290.09219.5100
4.11-4.7511.20.0797.41198610740.0250.07923.3100
4.75-5.8111.10.0936.5100289050.030.09324.1100
5.81-8.2210.80.0886.777667180.0280.0882499.8
8.22-48.4289.70.0727.239124020.0260.07228.296.3

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0017refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementResolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.765 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 549 4.7 %RANDOM
Rwork0.2347 ---
obs0.2373 11232 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.81 Å2 / Biso mean: 52.415 Å2 / Biso min: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 5 1727
Biso mean---55.08 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021775
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9442436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99324.67577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83715263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.199156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211369
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 40 -
Rwork0.401 720 -
all-760 -
obs--89.41 %

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