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- PDB-6wk4: Fab Fragment of Anti-human LAG3 antibody (13E2) -

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Basic information

Entry
Database: PDB / ID: 6wk4
TitleFab Fragment of Anti-human LAG3 antibody (13E2)
Components
  • 13E2 Fab Heavy Chain
  • 13E2 Fab Light Chain
KeywordsIMMUNE SYSTEM / Anti Human LAG3
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAgnihotri, P. / Mishra, A.K. / Mariuzza, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI144422-01 United States
CitationJournal: To Be Published
Title: Fab Fragment of Anti-human LAG3 antibody
Authors: Agnihotri, P. / Mishra, A.K. / Mariuzza, R.A.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 13E2 Fab Heavy Chain
B: 13E2 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3393
Polymers49,2172
Non-polymers1221
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Hetero-2-mer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-19 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.151, 74.048, 189.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody 13E2 Fab Heavy Chain


Mass: 25579.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 13E2 Fab Light Chain


Mass: 23637.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, potassium citrate tribasic / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0059 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2019 / Details: Sagitally focusing 2nd crystal
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: water cooled;
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0059 Å / Relative weight: 1
ReflectionResolution: 2.1→39.63 Å / Num. obs: 28514 / % possible obs: 98.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.05 / Rrim(I) all: 0.08 / Χ2: 0.96 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2176 / CC1/2: 0.73 / Rpim(I) all: 0.23 / Rrim(I) all: 0.47 / Χ2: 0.95 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.17.1_3660refinement
Aimlessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mim

1mim


Resolution: 2.1→39.63 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5418
RfactorNum. reflection% reflection
Rfree0.2284 1390 4.88 %
Rwork0.1862 --
obs0.1882 28503 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 8 263 3543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663358
X-RAY DIFFRACTIONf_angle_d0.90754579
X-RAY DIFFRACTIONf_chiral_restr0.053526
X-RAY DIFFRACTIONf_plane_restr0.0054579
X-RAY DIFFRACTIONf_dihedral_angle_d8.152463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.31511280.25322557X-RAY DIFFRACTION93.65
2.18-2.260.30141190.23162633X-RAY DIFFRACTION95.76
2.26-2.370.27761470.2312661X-RAY DIFFRACTION98.01
2.37-2.490.29311390.22222683X-RAY DIFFRACTION98.33
2.49-2.650.28551460.22122733X-RAY DIFFRACTION98.7
2.65-2.850.28871420.22732703X-RAY DIFFRACTION98.58
2.85-3.140.28821600.20952700X-RAY DIFFRACTION98.79
3.14-3.590.19961440.18832735X-RAY DIFFRACTION98.49
3.59-4.530.19741360.14742796X-RAY DIFFRACTION99.32
4.53-39.630.15591290.15412912X-RAY DIFFRACTION98.8

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