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- PDB-6wkl: Fab Fragment of Anti-human LAG3 antibody (BAP050) -

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Basic information

Entry
Database: PDB / ID: 6wkl
TitleFab Fragment of Anti-human LAG3 antibody (BAP050)
Components
  • BAP050 Fab Heavy Chain
  • BAP050 Fab Light Chain
KeywordsIMMUNE SYSTEM / Anti Human LAG3
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 16, 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: BAP050 Fab Heavy Chain
B: BAP050 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6873
Polymers49,5652
Non-polymers1221
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-21 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.770, 75.530, 103.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody BAP050 Fab Heavy Chain


Mass: 25862.857 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 BAP050 Fab Light Chain


Mass: 23702.148 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.: 447 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, HEPES Na / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.89→45.31 Å / Num. obs: 41427 / % possible obs: 97 % / Redundancy: 3 % / Biso Wilson estimate: 27.76 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.095 / Rrim(I) all: 0.13 / Χ2: 0.95 / Net I/σ(I): 5.9
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / Num. unique obs: 2239 / CC1/2: 0.23 / Rpim(I) all: 0.89 / Χ2: 0.92 / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mim

1mim


Resolution: 1.89→45.31 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 2005 4.84 %
Rwork0.1932 39387 -
obs0.1947 41392 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.23 Å2
Refinement stepCycle: LAST / Resolution: 1.89→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 8 448 3796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713426
X-RAY DIFFRACTIONf_angle_d0.89094667
X-RAY DIFFRACTIONf_chiral_restr0.0542524
X-RAY DIFFRACTIONf_plane_restr0.0054596
X-RAY DIFFRACTIONf_dihedral_angle_d8.3494472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.33091320.31972362X-RAY DIFFRACTION82.42
1.94-1.990.34571440.29282686X-RAY DIFFRACTION93.9
1.99-2.050.29641250.27012794X-RAY DIFFRACTION96.91
2.05-2.120.2541360.24652773X-RAY DIFFRACTION96.55
2.12-2.190.27291500.22992827X-RAY DIFFRACTION97.99
2.19-2.280.28771250.21872844X-RAY DIFFRACTION97.95
2.28-2.380.23431510.21532790X-RAY DIFFRACTION97.64
2.39-2.510.25481450.20932856X-RAY DIFFRACTION97.66
2.51-2.670.25231480.20922807X-RAY DIFFRACTION97.33
2.67-2.870.25931470.21012860X-RAY DIFFRACTION98.72
2.87-3.160.23911310.19252891X-RAY DIFFRACTION98.21
3.16-3.620.20781500.17272918X-RAY DIFFRACTION99.13
3.62-4.560.17581480.15122952X-RAY DIFFRACTION99.2
4.56-45.310.16741730.16333027X-RAY DIFFRACTION98.01

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