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- PDB-5hsf: 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1. -

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Basic information

Entry
Database: PDB / ID: 5hsf
Title1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Fc fragment / IgG1 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
TRIETHYLENE GLYCOL / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Flores, K. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Flores, K. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3384
Polymers30,0372
Non-polymers3002
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-10 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.713, 43.880, 49.579
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 15018.581 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: P01857
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.73 Å3/Da / Density % sol: 28.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 11.0 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3); Screen: PEGs II (F4), 0.2M Ammonium sulfate, 0.1M Sodium acetate, 22% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2010 / Details: Si(111)
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 31266 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.719 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.3
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-1HZH

1hzh


Resolution: 1.52→27.44 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.252 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18832 1570 5 %RANDOM
Rwork0.15721 ---
obs0.15875 29684 98.61 %-
Solvent computationIon probe radii: 0.6 Å / Shrinkage radii: 0.6 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.301 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å2-1.17 Å2
2---1.16 Å20 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.52→27.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 17 160 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192026
X-RAY DIFFRACTIONr_bond_other_d0.0010.021837
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9592781
X-RAY DIFFRACTIONr_angle_other_deg0.85534287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2655262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1525.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.05615340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.063159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212414
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5511.756988
X-RAY DIFFRACTIONr_mcbond_other1.5451.753987
X-RAY DIFFRACTIONr_mcangle_it2.5652.6181270
X-RAY DIFFRACTIONr_mcangle_other2.5642.6211271
X-RAY DIFFRACTIONr_scbond_it2.2622.0821038
X-RAY DIFFRACTIONr_scbond_other2.2612.0821038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4972.9911512
X-RAY DIFFRACTIONr_long_range_B_refined6.25514.7482182
X-RAY DIFFRACTIONr_long_range_B_other6.1314.1262119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.521→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 102 -
Rwork0.254 1973 -
obs--89.06 %
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)
11.3297-0.6275-0.20795.00120.08822.5018-0.205-0.2440.11510.28710.1726-0.58150.1420.25740.03240.10420.0145-0.00180.13860.0020.1398-11.15553.447-7.1316
23.1811-1.1268-0.7833.39540.58331.0671-0.0080.00250.1137-0.1209-0.0074-0.09210.02930.02580.01550.03720.0070.01370.03240.00530.0109-16.16554.9827-11.6994
33.8860.78210.16874.0438-2.02787.3322-0.0003-0.073-0.0399-0.04160.09750.22470.4207-0.3688-0.09710.027-0.02450.00390.0323-0.00960.034-28.2392.262-10.0644
41.5025-0.3017-0.47611.68940.18971.0126-0.0476-0.0080.0149-0.0327-0.0058-0.08580.03350.04780.05340.01690.00810.01160.0418-0.00290.0171-17.54753.8073-11.1003
53.5749-5.4929-1.741210.93632.59751.0383-0.1521-0.19090.02590.36610.0612-0.06140.14820.06260.0910.077-0.00260.02940.0577-0.01730.0645-19.0309-1.6075-2.0093
61.387-0.51171.67390.3418-1.15424.5519-0.0795-0.05510.04250.03190.1072-0.0313-0.2164-0.2988-0.02760.0903-0.0047-0.01190.0848-0.00060.0694-18.347718.4296-18.9265
71.4416-0.69080.95621.9327-1.74073.1546-0.0763-0.0014-0.04880.04760.0086-0.178-0.11960.12640.06770.021-0.001-0.00890.03150.00120.0474-8.842511.7345-12.1826
88.3749-1.16181.81744.38330.29092.56310.00450.08970.0528-0.38970.0004-0.3872-0.26270.2896-0.0050.0595-0.03410.02380.08630.02690.06923.946518.1528-12.6987
91.18210.17120.41471.4797-0.57592.4135-0.0338-0.03450.01360.005-0.0602-0.234-0.11290.17470.0940.0062-0.0069-0.00050.05090.010.0402-6.803913.6802-14.3599
101.3727-1.013.15152.0081-4.258610.47590.0024-0.08180.04650.21590.07370.0288-0.4783-0.0771-0.0760.1835-0.03770.00910.1137-0.02340.1229-6.828724.0821-11.9942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A315 - 331
2X-RAY DIFFRACTION2A332 - 354
3X-RAY DIFFRACTION3A355 - 365
4X-RAY DIFFRACTION4A366 - 406
5X-RAY DIFFRACTION5A407 - 419
6X-RAY DIFFRACTION6B312 - 328
7X-RAY DIFFRACTION7B329 - 354
8X-RAY DIFFRACTION8B355 - 363
9X-RAY DIFFRACTION9B364 - 406
10X-RAY DIFFRACTION10B407 - 419

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