A: Immunoglobulin heavy constant gamma 1 B: Immunoglobulin heavy constant gamma 1 R: DNA-binding protein 7d S: DNA-binding protein 7d C: Immunoglobulin heavy constant gamma 1 D: Immunoglobulin heavy constant gamma 1 T: DNA-binding protein 7d U: DNA-binding protein 7d
Evidence: gel filtration, The assembly contains two Fc-fragments (four heavy chains) and four nanofitin molecules
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
12430 Å2
ΔGint
-50 kcal/mol
Surface area
54740 Å2
Unit cell
Length a, b, c (Å)
68.270, 136.840, 69.760
Angle α, β, γ (deg.)
90.00, 90.12, 90.00
Int Tables number
4
Space group name H-M
P1211
-
Components
#1: Protein
Immunoglobulinheavyconstantgamma1 / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma- ...Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE
Mass: 24780.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal residues 228 - 235 of the sequence represent the methionine from the start codon followed by the affinity tag (His6-tag). Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli B (bacteria) / Strain (production host): Origami B / References: UniProt: P01857
#2: Protein
DNA-bindingprotein7d / 7 kDa DNA-binding protein d / Sac7d
Mass: 7887.911 Da / Num. of mol.: 4 Mutation: K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D Source method: isolated from a genetically manipulated source Details: The N-terminal residues DAEF were attached to the sequence for cloning purposes. We have named the mutation at position 24 "C24A" because it is based on the previously published Sac7d-C3 ...Details: The N-terminal residues DAEF were attached to the sequence for cloning purposes. We have named the mutation at position 24 "C24A" because it is based on the previously published Sac7d-C3 variant. Since we used here the wild-type sequence of Sac7d in UniProt for reference, this mutation is designated as W24A. Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Gene: Saci_0064 / Production host: Escherichia coli B (bacteria) / Strain (production host): NEB Express / References: UniProt: P13123
Has protein modification
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24 % (w/v) PEG8000, 0.1 M Tris/HCl pH 8.5
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
Detector
Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2024
Radiation
Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→69.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 31.514 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27928
1379
5 %
RANDOM
Rwork
0.22729
-
-
-
obs
0.22991
26198
97.02 %
-
Solvent computation
Ion probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: MASK