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- PDB-8uro: Crystal structure of IgG1-Fc fragment (E382S) in complex with Cor... -

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Basic information

Entry
Database: PDB / ID: 8uro
TitleCrystal structure of IgG1-Fc fragment (E382S) in complex with Corynebacterial ENGase CU43 (D187A-E189A)
Components
  • Corynebacterial protease CP40
  • Immunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / IgG1-Fc / CU43 / Endoglycosidase / IgG-specific
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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesCorynebacterium ulcerans (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsSastre, D.E. / Sultana, N. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI149297 United States
CitationJournal: To Be Published
Title: Crystal structure of IgG1-Fc fragment (E382S) in complex with Corynebacterial ENGase CU43 (D187A-E189A)
Authors: Sastre, D.E. / Sultana, N. / Sundberg, E.J.
History
DepositionOct 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corynebacterial protease CP40
B: Immunoglobulin gamma-1 heavy chain
C: Immunoglobulin gamma-1 heavy chain
D: Corynebacterial protease CP40
E: Immunoglobulin gamma-1 heavy chain
F: Immunoglobulin gamma-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)196,5536
Polymers196,5536
Non-polymers00
Water00
1
A: Corynebacterial protease CP40
B: Immunoglobulin gamma-1 heavy chain
C: Immunoglobulin gamma-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)98,2763
Polymers98,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Corynebacterial protease CP40
E: Immunoglobulin gamma-1 heavy chain
F: Immunoglobulin gamma-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)98,2763
Polymers98,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.439, 81.991, 148.099
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Corynebacterial protease CP40


Mass: 46107.309 Da / Num. of mol.: 2 / Mutation: D187A, E189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ulcerans (bacteria) / Gene: cpp, CULC0211_20780 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A830QWM5
#2: Antibody
Immunoglobulin gamma-1 heavy chain


Mass: 26084.551 Da / Num. of mol.: 4 / Mutation: E382S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
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: 3.53 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate 0.1 M MES 6.5 30 %v/v Glycerol ethoxylate (MIDAS 2-31)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 30847 / % possible obs: 98.7 % / Redundancy: 7 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.219 / Χ2: 0.501 / Net I/σ(I): 6.2
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.333 / Num. unique obs: 1554 / CC1/2: 0.747 / CC star: 0.925 / Rpim(I) all: 0.38 / Χ2: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.62→33.96 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 39.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3689 1948 6.46 %
Rwork0.3338 --
obs0.3362 30141 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.62→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9190 0 0 0 9190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029373
X-RAY DIFFRACTIONf_angle_d0.53412842
X-RAY DIFFRACTIONf_dihedral_angle_d4.0391412
X-RAY DIFFRACTIONf_chiral_restr0.0411542
X-RAY DIFFRACTIONf_plane_restr0.0031690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.62-3.710.50341150.38851727X-RAY DIFFRACTION82
3.71-3.820.36631520.35091970X-RAY DIFFRACTION95
3.82-3.930.38851300.33092002X-RAY DIFFRACTION96
3.93-4.050.38111390.32281998X-RAY DIFFRACTION96
4.05-4.20.35741320.33082046X-RAY DIFFRACTION97
4.2-4.370.36631420.32362050X-RAY DIFFRACTION98
4.37-4.560.33011360.30472065X-RAY DIFFRACTION98
4.56-4.80.33441510.322076X-RAY DIFFRACTION99
4.8-5.10.33091460.31142054X-RAY DIFFRACTION99
5.1-5.50.38551410.32672077X-RAY DIFFRACTION99
5.5-6.050.36881390.34362053X-RAY DIFFRACTION97
6.05-6.920.41761320.34211828X-RAY DIFFRACTION86
6.92-8.690.36911460.33512104X-RAY DIFFRACTION99
8.69-33.960.36341470.35152143X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.440.1034-1.09060.0226-0.04150.90330.8930.10780.0884-0.61240.5932-0.36550.22810.3250.53731.14820.2869-0.17041.05340.01561.185458.1798-19.4909-9.7167
20.5829-0.1182-0.24530.65180.9891.4760.3334-0.0853-0.36010.02010.57770.32730.6181-0.43082.02010.5598-0.1834-0.26690.51070.43181.177438.6757-1.077-25.6757
30.09290.01510.14570.03920.13730.63890.2458-0.1479-0.2251-0.26550.17640.56280.6327-0.94620.70731.3222-0.2677-0.68810.87060.20021.104438.0964-6.2422-29.0549
40.4815-0.07180.19770.60910.80281.24530.3807-0.0441-0.3780.4667-0.05890.12470.9242-0.1509-0.52281.08490.1882-0.48510.40930.18990.860843.1313-11.1426-25.7854
50.9332-0.227-0.52131.059-1.55893.08520.7-0.0572-0.9869-0.51070.56440.34370.4075-0.87651.6081.2348-0.2062-0.31910.85010.10050.78543.5717-22.2371-17.2783
60.31430.1021-0.20380.2857-0.1920.2532-0.14720.0587-0.3596-0.41950.1516-0.04460.1501-0.10460.1070.9833-0.2663-0.42090.4660.23190.991347.1642-23.9445-10.92
71.3391-0.09440.09970.5064-0.16281.5110.5063-0.3058-0.3237-0.24330.58270.04150.16990.38951.42920.29580.26190.34920.6125-0.27880.85853.182-13.203-17.5194
80.35830.1624-0.51440.26150.06541.27360.21790.24680.1782-0.48030.37360.2391-0.6628-0.22170.35690.9480.0501-0.07480.2746-0.09690.510350.8887-4.7003-7.2574
90.73640.31440.09870.2843-0.29950.64480.1068-0.11750.21920.020.3028-0.1247-0.0214-0.420.61340.19340.22060.1591.41160.00381.019435.40277.2905-12.6035
100.3333-0.2316-0.52710.56080.46311.12140.4725-0.27690.59460.19680.64510.04970.08650.28432.5032-0.12420.58150.3296-0.07510.03910.86644.2487.3415-17.427
110.2228-0.35150.11850.5459-0.00470.1202-0.5913-0.43590.21260.51210.5170.2859-0.0051-0.0231-0.00010.63820.06450.00450.63070.03660.751958.6819-22.101316.4611
120.0862-0.06170.0560.0472-0.04270.0403-0.0640.12090.21780.03820.0748-0.0673-0.01550.18180.2620.2092-0.24360.37280.9890.4941.01958.932-29.213212.5248
130.4807-0.37740.59590.9853-0.77060.8214-0.3046-0.40430.96480.1596-0.2209-0.2305-0.41670.0958-0.08960.5666-0.05310.01710.78580.0030.851564.6686-16.218618.8592
141.4315-0.521-1.22140.18480.44191.04980.83040.0271-0.0876-0.6181-0.2546-0.32830.02620.25030.3991.05750.0726-0.28370.75880.11680.684756.4753-18.09578.3163
150.0373-0.007-0.0190.00510.00370.0397-0.0875-0.3060.136-0.09020.30480.3256-0.00910.00070.0041.05410.0791-0.56650.6702-0.12561.450255.3028-0.971333.2584
160.0020.00370.0050.00180.00330.0089-0.2377-0.29-0.27380.3702-0.07380.09140.08650.374500.92770.12040.1621.3133-0.34560.723643.306-12.700357.2806
170.4802-0.3855-0.05050.36620.14610.20750.43360.35050.6556-0.0928-0.2871-0.0793-0.43730.15660.47430.4915-0.2390.50480.9368-0.1140.672552.9808-10.026539.1608
180.0194-0.1386-0.01220.4072-0.01760.15860.1713-0.93160.61340.6745-0.11070.3350.35530.142-0.01750.6681-0.1820.17821.0462-0.08920.83252.1877-11.443749.3642
190.47080.08360.09640.3696-0.12150.35680.1535-0.2906-0.0212-0.0419-0.0899-0.35240.01680.07860.15070.28770.52520.11771.413-0.29050.562261.2471-6.330640.8205
200.2839-0.6678-0.15571.64010.44680.12220.166-0.2619-0.3727-0.41640.07340.3235-0.46060.06920.02331.0783-0.26620.72151.05060.60812.269622.0131-18.121422.1525
21-0.01190.0138-0.0454-0.0068-0.00570.03550.0315-0.901-0.0407-0.21350.31350.0007-0.1805-0.32650.00021.1046-0.07960.20111.66750.26661.206620.0771-18.578629.4148
222.2884-0.46251.67971.412-0.19421.63430.1041-1.26130.23390.81610.75890.0605-0.90620.6531.98161.041-0.31820.57451.0161-0.16660.930536.2739-10.007542.1033
230.5931-0.860.06891.2942-0.070.80030.2353-0.39630.44810.03060.70340.2106-0.5032-0.56661.52230.4643-0.23760.75171.1743-0.36251.145336.5793-6.562544.8663
241.3817-1.06630.39783.2263-0.89750.4797-0.6774-0.2075-0.15120.6310.5299-0.1257-1.30770.0522-0.10611.0099-0.4877-0.28240.48990.05910.7206-34.9106-2.211549.8675
251.0226-0.3975-0.50851.0023-0.54170.89350.25980.4236-0.1717-0.2208-0.04080.16190.3509-0.20920.24651.3687-0.3630.23591.4853-0.30740.5085-33.1998-12.701823.2894
261.8005-0.4151-1.05770.3144-0.00840.9482-0.2146-0.2928-0.36110.0710.0004-0.3203-0.19580.2789-0.39561.1256-0.5013-0.1210.6607-0.01260.6078-37.2843-6.371930.8571
270.6649-0.09170.09980.3064-0.09120.03930.46760.1137-0.1214-0.84280.20270.37640.26880.04560.54141.09-0.3199-0.14930.9287-0.03430.6556-36.8783-0.635937.2205
280.45380.0879-0.1760.24250.31990.84520.41080.21560.2967-0.07130.62380.5314-0.4512-0.18693.03821.2354-0.5884-0.22430.84190.49770.8697-32.641415.605742.8903
290.5132-0.6527-0.10921.55340.45920.18580.08520.2264-0.0949-0.7780.0691.0467-0.1254-0.2789-0.02590.7062-0.2274-0.10480.64930.12060.5269-30.46962.615142.3669
300.17780.04730.13890.42920.07330.11910.0938-0.02550.2092-0.19540.21970.3287-0.08750.24780.35721.034-0.53120.3130.61420.07660.5646-28.318211.612249.7694
310.07840.14120.26540.18780.37891.3581-0.549-0.03990.30510.03540.45090.3493-0.65970.5946-0.0190.85780.04050.00590.43690.05910.6374-36.97660.711450.2044
320.01370.01680.14710.09490.23830.5677-0.6220.1063-0.1588-0.330.3932-0.0247-0.97370.265-0.01450.6573-0.02910.00050.53520.08010.9135-27.9926-7.308254.6638
330.0440.01360.03290.00390.02550.0828-0.55320.0978-0.4695-0.11230.5821-0.16030.11860.6963-0.00071.4892-0.16870.09271.2973-0.38251.0529-22.6813-20.240939.8358
340.949-0.8463-0.31041.11230.40180.1181-0.64830.2589-0.543-0.05680.3091-0.40040.06370.811-0.07460.4404-0.31110.19570.6323-0.2670.7041-31.7959-19.810643.4825
350.6860.3565-0.10040.6596-0.45591.0456-0.4419-0.0545-0.5590.00370.9746-0.05061.19520.16110.24370.96810.12720.11570.57510.04510.7732-14.98411.065375.4085
360.60660.3271-0.50351.085-0.55620.5481-0.8513-0.6886-0.04660.1005-0.08420.57650.52040.4334-1.5331.27610.5422-0.27950.9276-0.02250.5663-1.7183-0.696178.0706
370.265-0.3654-0.65250.7750.48832.26130.24290.0713-0.26690.21690.41680.1508-0.45930.88570.53981.14740.84140.16581.30020.16750.71649.1209-1.246389.4575
381.76250.4450.7771.85822.27152.8280.1281-0.1419-0.22550.39180.9155-0.28580.48380.65311.21791.08360.28190.44111.04830.63711.256717.27257.196954.2276
390.0741-0.01420.0170.0372-0.030.00490.77750.673-0.1523-0.5097-0.1230.1006-0.2836-0.37730.00281.9035-0.00950.24660.86120.17271.077515.244112.903344.8136
401.1335-0.4120.63791.5963-1.00610.74490.70480.31870.3296-0.00140.4518-0.10990.17670.08820.16421.79130.76590.40032.3338-0.17980.958819.10369.533152.5991
410.34930.17020.0570.4834-0.29950.2069-0.3357-0.02170.07980.0750.18340.19670.27720.1408-0.11890.79360.32810.47071.2883-0.45860.888317.27813.665361.1933
420.7709-0.0422-0.3450.76270.05821.63280.1829-0.1892-0.06420.07640.6984-0.34920.18690.49421.94261.96820.95330.7261.4606-0.02820.779819.6261-5.95380.2343
430.1222-0.1441-0.16740.15630.1980.25050.06080.2222-0.5091-0.2664-0.1298-0.1458-0.30040.0672-0.22111.0211.51760.52491.44230.34791.132920.3534-6.300775.9689
440.33740.03010.15380.02840.02330.0815-0.3560.0235-0.1713-0.0812-0.04960.1927-0.10610.064-0.26082.07370.74930.09372.1094-0.69650.837430.8545-1.505874.4051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 122 )
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 245 )
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 291 )
9X-RAY DIFFRACTION9chain 'A' and (resid 292 through 311 )
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 369 )
11X-RAY DIFFRACTION11chain 'B' and (resid 237 through 279 )
12X-RAY DIFFRACTION12chain 'B' and (resid 280 through 301 )
13X-RAY DIFFRACTION13chain 'B' and (resid 302 through 314 )
14X-RAY DIFFRACTION14chain 'B' and (resid 315 through 337 )
15X-RAY DIFFRACTION15chain 'B' and (resid 338 through 351 )
16X-RAY DIFFRACTION16chain 'B' and (resid 352 through 363 )
17X-RAY DIFFRACTION17chain 'B' and (resid 364 through 403 )
18X-RAY DIFFRACTION18chain 'B' and (resid 404 through 423 )
19X-RAY DIFFRACTION19chain 'B' and (resid 424 through 443 )
20X-RAY DIFFRACTION20chain 'C' and (resid 238 through 295 )
21X-RAY DIFFRACTION21chain 'C' and (resid 296 through 314 )
22X-RAY DIFFRACTION22chain 'C' and (resid 315 through 388 )
23X-RAY DIFFRACTION23chain 'C' and (resid 389 through 443 )
24X-RAY DIFFRACTION24chain 'D' and (resid 36 through 71 )
25X-RAY DIFFRACTION25chain 'D' and (resid 72 through 93 )
26X-RAY DIFFRACTION26chain 'D' and (resid 94 through 122 )
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 150 )
28X-RAY DIFFRACTION28chain 'D' and (resid 151 through 175 )
29X-RAY DIFFRACTION29chain 'D' and (resid 176 through 196 )
30X-RAY DIFFRACTION30chain 'D' and (resid 197 through 212 )
31X-RAY DIFFRACTION31chain 'D' and (resid 213 through 245 )
32X-RAY DIFFRACTION32chain 'D' and (resid 246 through 291 )
33X-RAY DIFFRACTION33chain 'D' and (resid 292 through 311 )
34X-RAY DIFFRACTION34chain 'D' and (resid 312 through 369 )
35X-RAY DIFFRACTION35chain 'E' and (resid 236 through 314 )
36X-RAY DIFFRACTION36chain 'E' and (resid 315 through 372 )
37X-RAY DIFFRACTION37chain 'E' and (resid 373 through 441 )
38X-RAY DIFFRACTION38chain 'F' and (resid 239 through 270 )
39X-RAY DIFFRACTION39chain 'F' and (resid 271 through 295 )
40X-RAY DIFFRACTION40chain 'F' and (resid 302 through 315 )
41X-RAY DIFFRACTION41chain 'F' and (resid 316 through 351 )
42X-RAY DIFFRACTION42chain 'F' and (resid 352 through 379 )
43X-RAY DIFFRACTION43chain 'F' and (resid 382 through 426 )
44X-RAY DIFFRACTION44chain 'F' and (resid 427 through 443 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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