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- PDB-6wju: Fab Fragment of Anti-human LAG3 antibody (4A10) -

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Basic information

Entry
Database: PDB / ID: 6wju
TitleFab Fragment of Anti-human LAG3 antibody (4A10)
Components
  • 4A10 Fab Heavy Chain
  • 4A10 Fab Light Chain
KeywordsIMMUNE SYSTEM / Anti Human LAG3
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 14, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 4A10 Fab Light Chain
H: 4A10 Fab Heavy Chain
A: 4A10 Fab Light Chain
B: 4A10 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)98,5444
Polymers98,5444
Non-polymers00
Water19811
1
L: 4A10 Fab Light Chain
H: 4A10 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)49,2722
Polymers49,2722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area19520 Å2
MethodPISA
2
A: 4A10 Fab Light Chain
B: 4A10 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)49,2722
Polymers49,2722
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-26 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)258.050, 258.050, 258.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLNGLN(chain 'A' and (resid 1 through 23 or (resid 24...AC1 - 61 - 6
121PROPROSERSER(chain 'A' and (resid 1 through 23 or (resid 24...AC9 - 329 - 32
131LEULEUGLUGLU(chain 'A' and (resid 1 through 23 or (resid 24...AC38 - 21838 - 218
211ASPASPGLNGLN(chain 'L' and (resid 1 through 7 or resid 9...LA1 - 61 - 6
221PROPROSERSER(chain 'L' and (resid 1 through 7 or resid 9...LA9 - 329 - 32
231LEULEUGLUGLU(chain 'L' and (resid 1 through 7 or resid 9...LA38 - 21838 - 218
112GLNGLNGLUGLU(chain 'B' and (resid 3 through 30 or resid 34...BD3 - 303 - 30
122METMETTHRTHR(chain 'B' and (resid 3 through 30 or resid 34...BD34 - 7134 - 71
132ASNASNLYSLYS(chain 'B' and (resid 3 through 30 or resid 34...BD77 - 13377 - 133
142SERSERPROPRO(chain 'B' and (resid 3 through 30 or resid 34...BD136 - 217136 - 217
212GLNGLNGLUGLU(chain 'H' and ((resid 3 and (name N or name...HB3 - 303 - 30
222METMETTHRTHR(chain 'H' and ((resid 3 and (name N or name...HB35 - 7234 - 71
232ASNASNSERSER(chain 'H' and ((resid 3 and (name N or name...HB78 - 13577 - 134
242GLYGLYPROPRO(chain 'H' and ((resid 3 and (name N or name...HB138 - 218137 - 217

NCS ensembles :
ID
1
2

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Components

#1: Antibody 4A10 Fab Light Chain


Mass: 24095.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human)
#2: Antibody 4A10 Fab Heavy Chain


Mass: 25176.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Lithium sulphate, Tris-HCl / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→44.26 Å / Num. obs: 26760 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 77.41 Å2 / CC1/2: 0.8 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.09 / Rrim(I) all: 0.2 / Χ2: 7.5 / Net I/σ(I): 7
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4760 / CC1/2: 0.36 / Rpim(I) all: 0.33 / Rrim(I) all: 0.68 / Χ2: 1.03 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e2t

5e2t


Resolution: 3.1→44.26 Å / SU ML: 0.4463 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2871 1305 4.88 %
Rwork0.2283 25452 -
obs0.2312 26757 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.34 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6397 0 0 11 6408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356543
X-RAY DIFFRACTIONf_angle_d0.84168923
X-RAY DIFFRACTIONf_chiral_restr0.05051026
X-RAY DIFFRACTIONf_plane_restr0.00521143
X-RAY DIFFRACTIONf_dihedral_angle_d18.55262279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.36791370.30132783X-RAY DIFFRACTION99.86
3.22-3.370.33471310.2742786X-RAY DIFFRACTION99.9
3.37-3.550.33561560.26022780X-RAY DIFFRACTION99.97
3.55-3.770.3191410.2512778X-RAY DIFFRACTION99.93
3.77-4.060.30341560.2422807X-RAY DIFFRACTION99.9
4.06-4.470.23611270.20242822X-RAY DIFFRACTION100
4.47-5.110.23591480.18542832X-RAY DIFFRACTION99.83
5.12-6.440.26131410.21992864X-RAY DIFFRACTION99.73
6.44-44.260.30281680.22693000X-RAY DIFFRACTION99.69

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