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- PDB-6x3i: NNAS Fc mutant -

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Basic information

Entry
Database: PDB / ID: 6x3i
TitleNNAS Fc mutant
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / Antibody Fc / glycan engineering
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
beta-D-mannopyranose / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.268 Å
AuthorsWei, R. / Zhou, Y.F.
CitationJournal: Mabs / Year: 2020
Title: Engineered Fc-glycosylation switch to eliminate antibody effector function.
Authors: Zhou, Q. / Jaworski, J. / Zhou, Y. / Valente, D. / Cotton, J. / Honey, D. / Boudanova, E. / Beninga, J. / Rao, E. / Wei, R. / Mauriac, C. / Pan, C. / Park, A. / Qiu, H.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6233
Polymers25,0181
Non-polymers6052
Water64936
1
A: Immunoglobulin gamma-1 heavy chain
hetero molecules

A: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2466
Polymers50,0372
Non-polymers1,2094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3350 Å2
ΔGint0 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.091, 142.504, 75.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 25018.336 Da / Num. of mol.: 1 / Fragment: Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.268→50 Å / Num. obs: 13336 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Χ2: 1.046 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.27-2.356.80.97113051.0431100
2.35-2.457.30.76113051.0541100
2.45-2.567.40.5613091.0861100
2.56-2.697.40.40213211.0921100
2.69-2.867.40.26213161.0581100
2.86-3.087.40.18213221.0021100
3.08-3.397.30.1113291.0171100
3.39-3.887.30.07513341.031100
3.88-4.896.80.06613581.055199.9
4.89-506.60.05214371.017199.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1839refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVE

3ave


Resolution: 2.268→48.925 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 651 4.89 %
Rwork0.1783 12665 -
obs0.1803 13316 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.16 Å2 / Biso mean: 71.0965 Å2 / Biso min: 30.78 Å2
Refinement stepCycle: final / Resolution: 2.268→48.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 39 36 1737
Biso mean--108.31 53.9 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151751
X-RAY DIFFRACTIONf_angle_d1.0592382
X-RAY DIFFRACTIONf_chiral_restr0.043268
X-RAY DIFFRACTIONf_plane_restr0.005303
X-RAY DIFFRACTIONf_dihedral_angle_d15.568662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2685-2.44360.34051330.2587245099
2.4436-2.68950.26581400.22862494100
2.6895-3.07870.27191330.21352509100
3.0787-3.87850.23821240.19132542100
3.8785-48.9250.1711210.14672670100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.76560.02220.47842.06580.16780.1704-0.11670.32120.2719-0.20210.3020.6609-0.8052-0.4156-0.15060.69160.14510.00330.54660.16190.465612.851117.58866.7108
24.504-1.49690.45172.80620.03851.5309-0.31470.20070.588-0.00880.23950.4058-0.9696-0.5254-0.0131.09320.1022-0.16030.82620.20560.918511.711631.75744.11
32.2513-0.39980.27381.9625-0.83142.1225-0.2882-0.07250.83130.17630.2073-0.2258-1.1897-0.07730.00520.93150.0447-0.13860.52370.03540.598618.722624.70219.9991
44.303-0.1718-0.82072.05540.03222.4035-0.21710.5321-0.8274-0.0831-0.05980.05890.31490.00020.20170.38590.00790.0650.4206-0.07880.47545.4141-5.421312.1632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 264 )A236 - 264
2X-RAY DIFFRACTION2chain 'A' and (resid 265 through 301 )A265 - 301
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 336 )A302 - 336
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 444 )A337 - 444

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