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- PDB-8zcl: Ambient Temperature Crystal Structure of Fc Fragment of Human IgG... -

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Basic information

Entry
Database: PDB / ID: 8zcl
TitleAmbient Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / fusion protein / immunoglobin / 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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / 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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government119C132 Turkey
CitationJournal: Small Struct / Year: 2025
Title: Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap
Authors: Destan, E. / Turkut, E. / Aldeniz, A. / Kang, J. / Tosha, T. / Yabashi, M. / Yilmaz, B. / Timucin, C. / Matsuura, H. / Kawano, Y. / Cinkaya, I. / Demirci, H.
History
DepositionApr 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1554
Polymers47,2692
Non-polymers2,8862
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint58 kcal/mol
Surface area21880 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


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
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: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Sep 20, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→143.31 Å / Num. obs: 38860 / % possible obs: 96.9 % / Redundancy: 38.5 % / CC1/2: 0.85 / Net I/σ(I): 4.42
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2273 / CC1/2: 0.041

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→40.99 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1191 6.99 %
Rwork0.1787 --
obs0.1827 17036 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 195 90 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033621
X-RAY DIFFRACTIONf_angle_d0.5434940
X-RAY DIFFRACTIONf_dihedral_angle_d11.9511410
X-RAY DIFFRACTIONf_chiral_restr0.043597
X-RAY DIFFRACTIONf_plane_restr0.004608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.40071100.34951447X-RAY DIFFRACTION77
2.7-2.830.32641170.27611568X-RAY DIFFRACTION83
2.83-2.980.28071230.24951625X-RAY DIFFRACTION86
2.98-3.160.31481290.23271727X-RAY DIFFRACTION92
3.16-3.410.24481350.18911785X-RAY DIFFRACTION95
3.41-3.750.22751380.16851837X-RAY DIFFRACTION97
3.75-4.290.2011420.1581910X-RAY DIFFRACTION98
4.29-5.40.20491440.13281920X-RAY DIFFRACTION100
5.41-40.990.20471530.15382026X-RAY DIFFRACTION99
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)
12.8877-0.008-0.50261.705-0.01426.1732-0.56020.99250.5624-2.74910.3084-0.2955-0.29810.0536-0.00641.8109-0.27140.23970.65140.10420.6258-34.301612.65588.7042
25.74190.33021.92223.41780.19083.2263-0.1909-0.60380.48740.39810.02330.0463-0.0639-0.00610.15140.20460.00520.04360.3799-0.07480.3432-31.18316.943840.2241
35.1820.78931.19754.8323-2.1257.6759-0.10170.223-0.4204-0.5506-0.0774-0.05420.8266-0.81740.10060.2347-0.05610.04720.3669-0.09240.3239-10.7814-14.573320.2548
45.11760.219-1.87367.724-2.19021.2820.0221.4429-0.938-1.71720.19350.2424-0.32680.1798-0.2740.5665-0.01320.02250.9137-0.25320.5084-8.6383-15.46751.6284
57.9330.47016.70532.68870.38119.0411.00350.2019-0.8343-0.3348-0.17590.08670.5293-0.2057-0.89070.5016-0.0537-0.02850.6898-0.25510.5888-11.3414-19.06776.8065
64.69640.383-0.02286.3660.56569.04760.03570.84290.0991-0.533-0.0098-0.0485-0.43510.4337-0.05440.2308-0.03640.0510.4593-0.01350.3602-4.2938-10.923812.9235
77.65610.5242-3.25984.2392-0.3855.27930.0578-1.00550.12660.2793-0.09050.156-0.08350.007-0.0420.18020.0507-0.04150.376-0.01150.3172-21.6417-2.974342.0972
85.79430.8217-1.18996.2351-0.24033.7841-0.1361-0.4943-0.57920.22010.1024-0.03180.2738-0.19170.08690.15480.0327-0.01620.42220.03760.3428-22.9193-8.121939.2405
96.30274.8553-6.35183.7341-4.9236.4483-0.4251-1.0363-1.161-0.21040.13910.410.54470.51990.21990.4569-0.01260.04440.49580.14230.6164-22.3845-14.136847.0618
105.9371-1.3888-3.17132.57051.12451.7643-0.1936-0.8821-0.98110.5967-0.0711-0.3986-0.00150.33640.16250.35510.1623-0.08120.55490.10840.4243-12.2113-10.392743.904
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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