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Basic information

Entry
Database: PDB / ID: 8zck
TitleSerial Femtosecond Crystallography Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / fusion protein / immunoglobulin / N-glycans
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government119C132 Turkey
CitationJournal: To Be Published
Title: Serial Femtosecond Crystallography Structure of Fc Fragment of Human IgG1 from VEGF-Trap
Authors: Destan, E. / Demirci, H.
History
DepositionApr 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1554
Polymers47,2692
Non-polymers2,8862
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint55 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.470, 79.990, 143.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23634.676 Da / Num. of mol.: 2 / Fragment: Fc Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-3DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d3-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.1M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2→32.67 Å / Num. obs: 132583 / % possible obs: 100 % / Redundancy: 135.3 % / CC1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 4.49
Reflection shellResolution: 2→2.14 Å / Num. unique obs: 7163 / CC1/2: 0.47 / CC star: 0.41 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
CrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.2 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 859 2.42 %
Rwork0.1886 --
obs0.1896 35449 88.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 195 127 3646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043640
X-RAY DIFFRACTIONf_angle_d0.6814967
X-RAY DIFFRACTIONf_dihedral_angle_d12.6731419
X-RAY DIFFRACTIONf_chiral_restr0.072600
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.3661030.40094149X-RAY DIFFRACTION65
2.13-2.290.32081290.30625221X-RAY DIFFRACTION81
2.29-2.520.3231460.24145850X-RAY DIFFRACTION91
2.52-2.880.24141550.2066231X-RAY DIFFRACTION97
2.88-3.630.21421600.16936474X-RAY DIFFRACTION99
3.63-29.20.21660.1636665X-RAY DIFFRACTION98
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)
11.55670.35880.25542.0454-0.62674.5369-0.6670.73130.4354-3.60620.25640.0421-0.50320.2085-0.1892.3655-0.3770.26480.62340.12660.4695-34.24312.62268.5218
25.1540.5731.46573.30190.73433.4477-0.1809-0.6430.43680.2640.1085-0.0113-0.0388-0.0180.08390.21620.03310.02610.3349-0.06430.3645-31.15817.034940.2294
36.00860.03913.15983.6561-1.318.9126-0.02670.1077-0.4166-0.3072-0.03680.03740.4658-0.5686-0.00460.2693-0.04040.0380.3186-0.08410.4123-10.7824-14.526120.306
46.54421.25913.64246.77131.04332.0951-0.13911.5113-1.1539-1.38050.35880.0595-0.26790.6261-0.18110.6334-0.0684-0.01630.9673-0.24570.5182-8.7323-15.48531.6647
59.87353.48276.71824.40872.65655.12370.54850.7497-0.5447-0.2818-0.16860.04630.3646-0.0045-0.47150.5317-0.01940.02920.8098-0.22830.4699-11.3832-19.05046.8211
65.87740.71921.3634.91561.06691.9752-0.04830.94960.0494-0.63770.1613-0.2123-0.45670.674-0.11530.3497-0.07320.06870.4529-0.04640.3877-4.3114-10.89712.9411
72.4162-0.5007-4.42383.13420.16688.5052-0.1182-0.42090.24850.34530.24310.22740.047-0.0158-0.10320.27870.0632-0.01720.33330.00930.3416-21.4402-2.793442.2103
87.78391.0435-1.95035.7583-1.09574.2736-0.1517-0.4511-0.44820.24190.16140.38930.304-0.1690.02380.21250.0251-0.00190.33240.02650.3142-22.8858-8.044939.312
95.91475.9493-5.47766.753-5.05435.358-0.4235-1.0315-1.05670.31730.39150.49640.84060.06950.19180.52060.07050.08850.67120.24610.6913-22.3933-14.041947.1463
109.21681.0727-6.03194.512-0.81947.6348-0.1367-0.9164-0.51370.65720.2317-0.27140.15450.0626-0.07390.37830.1043-0.08810.5160.06080.3621-12.2099-10.291943.9926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 428 )
3X-RAY DIFFRACTION3chain 'B' and (resid 222 through 249 )
4X-RAY DIFFRACTION4chain 'B' and (resid 250 through 264 )
5X-RAY DIFFRACTION5chain 'B' and (resid 265 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 321 )
7X-RAY DIFFRACTION7chain 'B' and (resid 322 through 357 )
8X-RAY DIFFRACTION8chain 'B' and (resid 358 through 403 )
9X-RAY DIFFRACTION9chain 'B' and (resid 404 through 413 )
10X-RAY DIFFRACTION10chain 'B' and (resid 414 through 428 )

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