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- PDB-9dsj: Crystal structure of the cow antibody 105 -

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Basic information

Entry
Database: PDB / ID: 9dsj
TitleCrystal structure of the cow antibody 105
Components
  • 115 Fab heavy chain
  • 115 Fab light chain
KeywordsIMMUNE SYSTEM / neutralizing antibody
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFan, C. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI165075 United States
CitationJournal: To Be Published
Title: Crystal structure of the cow antibody 105
Authors: Fan, C. / Bjorkman, P.J.
History
DepositionSep 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 115 Fab heavy chain
L: 115 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4344
Polymers52,1782
Non-polymers2562
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-22 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.780, 154.705, 54.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11L-427-

HOH

21L-488-

HOH

31L-537-

HOH

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Components

#1: Antibody 115 Fab heavy chain


Mass: 29653.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#2: Antibody 115 Fab light chain


Mass: 22524.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.12 M alcohol, 0.1M buffer system 3 pH 8.5, 30% precipitant mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→38.68 Å / Num. obs: 72405 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 31.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 1.02 / Net I/σ(I): 16.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.031 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3410 / CC1/2: 0.421 / Rpim(I) all: 0.877 / Rrim(I) all: 3.16 / Χ2: 0.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.68 Å / SU ML: 0.1958 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2000 2.77 %
Rwork0.1665 70261 -
obs0.1678 72261 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.68 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 17 268 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523740
X-RAY DIFFRACTIONf_angle_d0.80915116
X-RAY DIFFRACTIONf_chiral_restr0.0535602
X-RAY DIFFRACTIONf_plane_restr0.0063653
X-RAY DIFFRACTIONf_dihedral_angle_d12.39791360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.32451370.26064807X-RAY DIFFRACTION96.71
1.69-1.740.25341410.22114939X-RAY DIFFRACTION99.71
1.74-1.790.28181410.20584965X-RAY DIFFRACTION99.75
1.79-1.840.26971410.19984956X-RAY DIFFRACTION99.82
1.84-1.910.21251410.16964992X-RAY DIFFRACTION99.92
1.91-1.990.19921440.15565018X-RAY DIFFRACTION99.86
1.99-2.080.23021430.14755027X-RAY DIFFRACTION99.9
2.08-2.190.20961410.15614967X-RAY DIFFRACTION99.98
2.19-2.320.20891430.17424995X-RAY DIFFRACTION99.98
2.32-2.50.23111420.1765023X-RAY DIFFRACTION99.29
2.5-2.750.23561430.18445021X-RAY DIFFRACTION99.38
2.75-3.150.23441460.18355095X-RAY DIFFRACTION99.89
3.15-3.970.21771450.16475133X-RAY DIFFRACTION99.87
3.97-38.680.17331520.14685323X-RAY DIFFRACTION99.35

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