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- PDB-3qhf: Crystal Structure of Fab del2D1, a deletion variant of anti-influ... -

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Basic information

Entry
Database: PDB / ID: 3qhf
TitleCrystal Structure of Fab del2D1, a deletion variant of anti-influenza antibody 2D1
Components
  • Human monoclonal antibody del2D1, Fab Heavy Chain
  • Human monoclonal antibody del2D1, Fab Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Immune recognition / Influenza A virus hemagglutinin / Extracellular (secreted)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: MBio / Year: 2011
Title: An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody.
Authors: Krause, J.C. / Ekiert, D.C. / Tumpey, T.M. / Smith, P.B. / Wilson, I.A. / Crowe, J.E.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: 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 13, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Human monoclonal antibody del2D1, Fab Heavy Chain
L: Human monoclonal antibody del2D1, Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,0992
Polymers47,0992
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.913, 69.680, 97.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Human monoclonal antibody del2D1, Fab Heavy Chain


Mass: 24304.389 Da / Num. of mol.: 1 / Fragment: Fab Heavy Chain / Mutation: deletion of somatic insertion (ITY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin gamma / Plasmid: pEE6.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody Human monoclonal antibody del2D1, Fab Light Chain


Mass: 22795.078 Da / Num. of mol.: 1 / Fragment: Fab Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin lambda / Plasmid: pEE12.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4000, 100 mM sodium acetate, and 200 mM magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: Double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 55866 / Num. obs: 55730 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.65→1.71 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QHZ (chains H and L)

3qhz


Resolution: 1.655→50 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2830 5.08 %Random
Rwork0.1831 ---
all0.1845 55866 --
obs0.1845 55730 98.1 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.462 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8687 Å20 Å2-0 Å2
2--4.8174 Å2-0 Å2
3---0.0513 Å2
Refinement stepCycle: LAST / Resolution: 1.655→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 273 3563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093475
X-RAY DIFFRACTIONf_angle_d1.2274766
X-RAY DIFFRACTIONf_dihedral_angle_d12.261241
X-RAY DIFFRACTIONf_chiral_restr0.078554
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.655-1.6830.3028860.2491867X-RAY DIFFRACTION69
1.683-1.71360.24071430.2332625X-RAY DIFFRACTION100
1.7136-1.74660.29091430.22922650X-RAY DIFFRACTION99
1.7466-1.78220.2291490.21032637X-RAY DIFFRACTION99
1.7822-1.8210.23561440.20742651X-RAY DIFFRACTION99
1.821-1.86340.21251470.20212619X-RAY DIFFRACTION99
1.8634-1.910.25391530.20132633X-RAY DIFFRACTION99
1.91-1.96160.27571290.1932698X-RAY DIFFRACTION99
1.9616-2.01930.20811370.1962627X-RAY DIFFRACTION99
2.0193-2.08450.22111600.18012655X-RAY DIFFRACTION99
2.0845-2.1590.21271380.18482675X-RAY DIFFRACTION99
2.159-2.24540.20821270.18252690X-RAY DIFFRACTION100
2.2454-2.34760.21721410.19132694X-RAY DIFFRACTION100
2.3476-2.47140.21871400.19142690X-RAY DIFFRACTION100
2.4714-2.62620.21941400.20862689X-RAY DIFFRACTION100
2.6262-2.8290.25831290.19742728X-RAY DIFFRACTION100
2.829-3.11360.19691240.1942736X-RAY DIFFRACTION100
3.1136-3.56390.21931800.18092700X-RAY DIFFRACTION100
3.5639-4.48950.19091400.15452787X-RAY DIFFRACTION100
4.4895-43.81180.1781800.17112849X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.94320.150.24342.40940.51944.1313-0.0823-0.1094-0.10560.09110.0819-0.15570.12380.21010.00310.13080.05860.01880.25950.05180.1965-0.5435-25.52938.2463
22.87370.2425-0.10222.9552-1.56423.1685-0.06650.22580.2194-0.1415-0.0756-0.05960.01390.170.1450.1893-0.0094-0.0220.18160.01870.17523.5423-14.7771-22.2556
33.0626-0.2290.04682.9253-0.30972.77180.2312-0.21710.43540.0224-0.196-0.1336-0.41620.1988-0.04770.2331-0.00910.03560.2787-0.00390.255-2.6215-5.612113.5923
42.0963-0.74080.02884.4433-0.63973.75580.06390.0227-0.05880.25460.11950.1569-0.0612-0.1007-0.16120.19780.00180.00950.1630.01840.1867-7.5946-3.9509-24.6762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:113
2X-RAY DIFFRACTION2chain H and resid 114:232
3X-RAY DIFFRACTION3chain L and resid 1:108
4X-RAY DIFFRACTION4chain L and resid 109:213

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