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- PDB-3dnk: Enzyme deglycosylated Human IgG1 Fc fragment -

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Basic information

Entry
Database: PDB / ID: 3dnk
TitleEnzyme deglycosylated Human IgG1 Fc fragment
ComponentsIGHM protein
KeywordsIMMUNE SYSTEM / Immunoglobulin fold
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBraden, B.C.
CitationJournal: To be Published
Title: 2.8 Angstrom structure of a enzyme deglycosylated human IgG1 Fc fragment
Authors: Braden, B.C.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGHM protein
B: IGHM protein


Theoretical massNumber of molelcules
Total (without water)48,0162
Polymers48,0162
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.37, 78.21, 147.15
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IGHM protein / Human IgG1 antibody Fc fragment-deglycosylated


Mass: 24008.123 Da / Num. of mol.: 2 / Fragment: UNP residues 267-478 / Mutation: N328D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Intact, humanized IgG1 Medi-524 produced in hybridomas. Fc fragment produced by papain digestion
Gene: IGHM / Production host: mus musculus (house mouse) / Strain (production host): mouse NSO cells / References: UniProt: Q6PI81, UniProt: P01857*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 20% PEG 6000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2004 / Details: Osmic mirrors
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. all: 13939 / Num. obs: 13869 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.84→2.94 Å / Rmerge(I) obs: 0.163 / % possible all: 82

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→20.08 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.32 1273 random
Rwork0.24 --
obs0.24 13869 -
all-13939 -
Refinement stepCycle: LAST / Resolution: 2.84→20.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 0 86 3433

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