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- PDB-3l7f: Structure of IL-13 antibody H2L6, A humanized variant OF C836 -

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Basic information

Entry
Database: PDB / ID: 3l7f
TitleStructure of IL-13 antibody H2L6, A humanized variant OF C836
Components
  • H2L6 HEAVY CHAIN
  • H2L6 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Human framework adaptation of a mouse anti-human IL-13 antibody.
Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, ...Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, S. / Zhao, Y. / Swanson, R.V. / Almagro, J.C.
History
DepositionDec 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: H2L6 LIGHT CHAIN
H: H2L6 HEAVY CHAIN
A: H2L6 LIGHT CHAIN
B: H2L6 HEAVY CHAIN
D: H2L6 LIGHT CHAIN
E: H2L6 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,12110
Polymers142,7926
Non-polymers3284
Water4,017223
1
L: H2L6 LIGHT CHAIN
H: H2L6 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7904
Polymers47,5972
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-48 kcal/mol
Surface area19060 Å2
MethodPISA
2
A: H2L6 LIGHT CHAIN
B: H2L6 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,5972
Polymers47,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-33 kcal/mol
Surface area19090 Å2
MethodPISA
3
D: H2L6 LIGHT CHAIN
E: H2L6 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7344
Polymers47,5972
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.640, 228.160, 234.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody H2L6 LIGHT CHAIN


Mass: 23487.115 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): Human embryonic kidney (HEK) 293 cells
Production host: Homo Sapiens (human)
#2: Antibody H2L6 HEAVY CHAIN


Mass: 24110.328 Da / Num. of mol.: 3
Fragment: FD fragment of the heavy chain, VH and CH1 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): Human embryonic kidney (HEK) 293 cells
Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES PH 6.5, 5% PEG 4K, 38% MPD; CRYO CONDITIONS: 0.1 M MES PH 6.5, 5% PEG 4K, 40% MPD, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 4, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→66.6 Å / Num. all: 56212 / Num. obs: 56212 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 92.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L5X

3l5x


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.473 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.279 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24264 2269 4.1 %RANDOM
Rwork0.20514 ---
all0.20667 53577 --
obs0.20667 53577 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error free: 0.279 Å
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9959 0 16 223 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210232
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.96313963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82351297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11424.4375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.076151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6831533
X-RAY DIFFRACTIONr_chiral_restr0.0870.21594
X-RAY DIFFRACTIONr_gen_planes_refined00.027612
X-RAY DIFFRACTIONr_nbd_refined0.2130.24249
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2483
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.24
X-RAY DIFFRACTIONr_mcbond_it2.93326631
X-RAY DIFFRACTIONr_mcangle_it5.156410579
X-RAY DIFFRACTIONr_scbond_it18.788884149
X-RAY DIFFRACTIONr_scangle_it19.22883384
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 148 -
Rwork0.229 3581 -
obs--92.8 %

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