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- PDB-7rho: Human IgG1 Fc fragment, hinge-free, expressed in E. coli -

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Basic information

Entry
Database: PDB / ID: 7rho
TitleHuman IgG1 Fc fragment, hinge-free, expressed in E. coli
ComponentsFc fragment of human IgG1
KeywordsIMMUNE SYSTEM / immunoglobulin Fc fragment / E. coli / bacterial expression / aglycosylated
Function / homology
Function and homology information


metal ion binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGallagher, D.T.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2023
Title: Effects of glycans and hinge on dynamics in the IgG1 Fc.
Authors: Bergonzo, C. / Hoopes, J.T. / Kelman, Z. / Gallagher, D.T.
History
DepositionJul 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fc fragment of human IgG1
B: Fc fragment of human IgG1
D: Fc fragment of human IgG1
E: Fc fragment of human IgG1
F: Fc fragment of human IgG1
G: Fc fragment of human IgG1
J: Fc fragment of human IgG1
K: Fc fragment of human IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,69510
Polymers193,2198
Non-polymers4772
Water11,962664
1
A: Fc fragment of human IgG1
B: Fc fragment of human IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5433
Polymers48,3052
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-13 kcal/mol
Surface area21890 Å2
MethodPISA
2
D: Fc fragment of human IgG1
E: Fc fragment of human IgG1


Theoretical massNumber of molelcules
Total (without water)48,3052
Polymers48,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-9 kcal/mol
Surface area21820 Å2
MethodPISA
3
F: Fc fragment of human IgG1
G: Fc fragment of human IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5433
Polymers48,3052
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-13 kcal/mol
Surface area21440 Å2
MethodPISA
4
J: Fc fragment of human IgG1
K: Fc fragment of human IgG1


Theoretical massNumber of molelcules
Total (without water)48,3052
Polymers48,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-9 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.836, 150.392, 241.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fc fragment of human IgG1


Mass: 24152.359 Da / Num. of mol.: 8 / Fragment: engineered variant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Plasmid: pET-15b / Production host: Enterobacteria phage L1 (virus) / Strain (production host): BL21(DE3) / References: UniProt: Q6MZV7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.45 % / Mosaicity: 0.12 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7 / Details: 20% (w/v) PEG 6000, 40 mM CaCl2, 100 mM NaHepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2→150.44 Å / Num. obs: 114393 / % possible obs: 88.5 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.026 / Rrim(I) all: 0.088 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.129.91.739100172101000.4640.5581.8311.155.2
6.35-150.449.80.0344396044730.9990.0110.03645.499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vgp

5vgp


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.494 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 5637 4.9 %RANDOM
Rwork0.2197 ---
obs0.2222 110541 88.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.22 Å2 / Biso mean: 54.095 Å2 / Biso min: 26.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.67 Å20 Å2
3---0.62 Å2
Refinement stepCycle: final / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13148 0 30 664 13842
Biso mean--74.94 56.73 -
Num. residues----1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213560
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.64718489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24551644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22223.975634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.046152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5161544
X-RAY DIFFRACTIONr_chiral_restr0.0990.21732
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210258
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 188 -
Rwork0.377 4022 -
all-4210 -
obs--44.81 %
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)
10.348-0.2732-0.02070.6759-0.36480.55750.0681-0.037-0.0673-0.1557-0.07710.14150.11170.02520.0090.19880.0168-0.01660.13220.01820.170242.120610.267629.1636
20.3486-0.05880.0960.8536-0.12780.2502-0.00830.07110.04150.13520.0931-0.00680.0057-0.0687-0.08470.15790.09910.02940.19830.04340.133257.478924.913947.1177
30.5162-0.56820.18250.8868-0.02220.2866-0.02530.01140.1374-0.1083-0.0195-0.1437-0.03760.08820.04480.205-0.01350.00340.18360.05110.132153.192545.075513.7771
40.13410.03570.28160.757-0.39120.983-0.035-0.0367-0.00630.01130.00720.1322-0.1012-0.05430.02780.18280.1061-0.04240.15050.00630.182329.012146.449229.7307
50.52260.1941-0.03380.70780.37930.49960.1024-0.1294-0.1390.0225-0.0874-0.13210.09680.0413-0.01490.1633-0.0428-0.03420.20380.04910.119733.908611.341191.4406
60.2743-0.20080.0070.88670.15640.41680.129-0.09230.093-0.0766-0.0249-0.15370.0065-0.1019-0.10410.1508-0.0470.0440.1753-0.00330.182318.06625.757572.9933
71.98970.65620.34060.9622-0.14280.8990.0858-0.3490.32340.1202-0.17680.1942-0.241-0.11920.0910.2037-0.03040.02440.3909-0.13080.080722.850745.7501106.9434
80.3083-0.25490.40090.790.27131.68350.02220.01890.0261-0.0863-0.1242-0.2061-0.26010.0120.1020.1854-0.1182-0.04160.14160.02490.22346.749847.14590.7108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A240 - 900
2X-RAY DIFFRACTION2B241 - 446
3X-RAY DIFFRACTION3D240 - 446
4X-RAY DIFFRACTION4E239 - 446
5X-RAY DIFFRACTION5F240 - 900
6X-RAY DIFFRACTION6G240 - 446
7X-RAY DIFFRACTION7J240 - 443
8X-RAY DIFFRACTION8K240 - 445

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